report.html

<title>Transcript QC</title><style>body{font-family:-apple-system,Segoe UI,Helvetica,Arial,sans-serif;max-width:1100px;margin:30px auto;padding:0 20px;color:#222}h1{margin-bottom:2px}.sub{color:#666}.cards{display:flex;gap:12px;flex-wrap:wrap;margin:18px 0}.card{border:1px solid #e5e5e5;border-radius:10px;padding:12px 16px;min-width:150px}.card b{font-size:22px;display:block}table{border-collapse:collapse;font-size:13px;width:100%}th,td{border-bottom:1px solid #eee;padding:5px 8px;text-align:left;vertical-align:top}tr.p td{background:#fff8f0}code{font-family:Menlo,Consolas,monospace;font-size:12px}.foot{color:#888;font-size:12px;margin-top:30px}details{margin:14px 0}</style>
<h1>Transcript QC</h1>
<p class=sub>14 transcripts checked against MANE v1.5 (bundled) · 2026-09-03</p>
<div class=cards>
<div class=card style='border-left:5px solid #c0392b'><b>1</b>✗ gene mismatch</div>
<div class=card style='border-left:5px solid #c0392b'><b>1</b>✗ unparseable</div>
<div class=card style='border-left:5px solid #e07a00'><b>1</b>⚠ mane select changed</div>
<div class=card style='border-left:5px solid #e07a00'><b>3</b>⚠ old version</div>
<div class=card style='border-left:5px solid #e07a00'><b>2</b>⚠ non mane</div>
<div class=card style='border-left:5px solid #7f8c8d'><b>1</b>? unknown gene</div>
<div class=card style='border-left:5px solid #2a9d8f'><b>5</b>✓ mane select</div>
<div class=card style='border-left:5px solid #c0392b'><b>9</b>potential reporting problems</div></div>
<p>ℹ Genes with a MANE Plus Clinical transcript in this set: <b>SCN2A</b> — check which isoform carries each variant.</p>
<table><tr><th></th><th>gene</th><th>input</th><th>variant</th><th>MANE Select</th><th>Plus Clinical</th><th>status</th><th>suggested check</th><th>note</th></tr>
<tr class='p'><td style='color:#c0392b;font-weight:700'>✗</td><td>BRCA1</td><td><code>NM_000059.4</code></td><td><code>c.100A&gt;G</code></td><td><code>NM_007294.4</code></td><td><code></code></td><td>GENE_MISMATCH</td><td>fix gene or transcript</td><td>NM_000059.4 is the MANE Select transcript of BRCA2, not BRCA1</td></tr>
<tr class='p'><td style='color:#c0392b;font-weight:700'>✗</td><td>FOO</td><td><code></code></td><td><code>c.1A&gt;G</code></td><td><code>—</code></td><td><code></code></td><td>UNPARSEABLE</td><td>fix the accession</td><td></td></tr>
<tr class='p'><td style='color:#e07a00;font-weight:700'>⚠</td><td>ACHE</td><td><code>NM_001302622.2</code></td><td><code>c.100A&gt;G</code></td><td><code>NM_000665.5</code></td><td><code></code></td><td>MANE_SELECT_CHANGED</td><td>move to the current MANE Select; re-map the variant</td><td>MANE Select changed in MANE v1.5: now NM_000665.5 (ENST00000241069.11), previously NM_001302622.2; CDS affected: No</td></tr>
<tr class='p'><td style='color:#e07a00;font-weight:700'>⚠</td><td>BRCA1</td><td><code>NM_007294.3</code></td><td><code>c.5266dupC</code></td><td><code>NM_007294.4</code></td><td><code></code></td><td>OLD_VERSION</td><td>update transcript version; re-validate c. position</td><td>current version is NM_007294.4</td></tr>
<tr class='p'><td style='color:#e07a00;font-weight:700'>⚠</td><td>BRCA2</td><td><code>NM_000059.3</code></td><td><code>c.5946delT</code></td><td><code>NM_000059.4</code></td><td><code></code></td><td>OLD_VERSION</td><td>update transcript version; re-validate c. position</td><td>current version is NM_000059.4</td></tr>
<tr class='p'><td style='color:#e07a00;font-weight:700'>⚠</td><td>MEFV</td><td><code>NM_000243.2</code></td><td><code>c.2080A&gt;G</code></td><td><code>NM_000243.3</code></td><td><code></code></td><td>OLD_VERSION</td><td>update transcript version; re-validate c. position</td><td>current version is NM_000243.3</td></tr>
<tr class='p'><td style='color:#e07a00;font-weight:700'>⚠</td><td>SCN2A</td><td><code>NM_021007.2</code></td><td><code>c.4766A&gt;G</code></td><td><code>NM_001040142.2</code></td><td><code>NM_001371246.1</code></td><td>NON_MANE</td><td>review transcript choice against MANE Select / MANE Plus Clinical; document the rationale if retaining a non-MANE transcript</td><td>gene has MANE Plus Clinical transcript(s): NM_001371246.1 — check which isoform carries the variant</td></tr>
<tr class='p'><td style='color:#e07a00;font-weight:700'>⚠</td><td>TTN</td><td><code>NM_133378.4</code></td><td><code>c.100A&gt;G</code></td><td><code>NM_001267550.2</code></td><td><code></code></td><td>NON_MANE</td><td>review transcript choice against MANE Select / MANE Plus Clinical; document the rationale if retaining a non-MANE transcript</td><td></td></tr>
<tr class='p'><td style='color:#7f8c8d;font-weight:700'>?</td><td>NOTAGENE</td><td><code>NM_000000.1</code></td><td><code>c.1A&gt;G</code></td><td><code>—</code></td><td><code></code></td><td>UNKNOWN_GENE</td><td>check the gene symbol</td><td></td></tr>
<tr class=''><td style='color:#2a9d8f;font-weight:700'>✓</td><td>TP53</td><td><code>NM_000546.6</code></td><td><code>c.743G&gt;A</code></td><td><code>NM_000546.6</code></td><td><code></code></td><td>MANE_SELECT</td><td>none</td><td></td></tr>
<tr class=''><td style='color:#2a9d8f;font-weight:700'>✓</td><td>SCN2A</td><td><code>NM_001040142.2</code></td><td><code>c.4766A&gt;G</code></td><td><code>NM_001040142.2</code></td><td><code>NM_001371246.1</code></td><td>MANE_SELECT</td><td>none</td><td>gene has MANE Plus Clinical transcript(s): NM_001371246.1 — check which isoform carries the variant</td></tr>
<tr class=''><td style='color:#2a9d8f;font-weight:700'>✓</td><td>CFTR</td><td><code>NM_000492.4</code></td><td><code>c.1521_1523delCTT</code></td><td><code>NM_000492.4</code></td><td><code></code></td><td>MANE_SELECT</td><td>none</td><td></td></tr>
<tr class=''><td style='color:#2a9d8f;font-weight:700'>✓</td><td>TTN</td><td><code>NM_001267550.2</code></td><td><code>c.100A&gt;G</code></td><td><code>NM_001267550.2</code></td><td><code></code></td><td>MANE_SELECT</td><td>none</td><td></td></tr>
<tr class=''><td style='color:#2a9d8f;font-weight:700'>✓</td><td>MYH7</td><td><code>ENST00000355349.4</code></td><td><code>c.100A&gt;G</code></td><td><code>NM_000257.4</code></td><td><code></code></td><td>MANE_SELECT</td><td>none</td><td></td></tr>
</table><details><summary>What the statuses mean</summary><ul><li><b>MANE_SELECT</b> — matches the current MANE Select transcript — aligned with the MANE reference set</li><li><b>MANE_PLUS_CLINICAL</b> — a MANE Plus Clinical transcript — acceptable when this isoform is the clinically relevant one; say why</li><li><b>OLD_VERSION</b> — right transcript, outdated version — c. coordinates may differ; update the version and re-check the HGVS</li><li><b>OLD_VERSION_PLUS_CLINICAL</b> — a MANE Plus Clinical transcript at an outdated version — update the version</li><li><b>NEWER_VERSION</b> — a version newer than the MANE snapshot — update the MANE snapshot before deciding</li><li><b>MANE_SELECT_CHANGED</b> — this used to be MANE Select; the current MANE Select is a different accession — check coordinates carefully</li><li><b>NON_MANE</b> — not a MANE transcript for this gene — review the transcript choice against MANE Select / MANE Plus Clinical; a non-MANE transcript can be legitimate with a documented rationale</li><li><b>GENE_MISMATCH</b> — the transcript belongs to a different gene than stated — likely a copy-paste error</li><li><b>GENE_NOT_IN_MANE</b> — protein-coding gene without a MANE transcript yet — no MANE reference to compare against</li><li><b>UNKNOWN_TRANSCRIPT</b> — accession not in the MANE snapshot and no gene given — cannot tell which gene it belongs to (add a gene column)</li><li><b>UNKNOWN_GENE</b> — gene symbol not found in MANE — check the symbol (HGNC) or spelling</li><li><b>UNPARSEABLE</b> — could not parse the transcript accession</li></ul></details>
<p class=foot>transcriptqc · MANE v1.5 (bundled) from NCBI/EBI bulk files (offline, reproducible). A transcript check, not a variant classification.</p>