missing hgnc id for several variants

[hmcostello]

Describe the bug

When querying the variation/normalize endpoint for some x-chromosome variants, no gene symbols or gene IDs were returned. Here are the variants:

X-118725211-A-G
X-101395767-C-T
X-10096159-C-T

I used the docker version of the normalizer, and I had GRCh37 input data.

example of output:

{
"warnings": [],
"service_meta_": {
"name": "variation-normalizer",
"version": "0.15.0",
"response_datetime": "2025-07-28T17:58:54.658145Z",
"url": "https://github.com/cancervariants/variation-normalization"
},
"variation_query": "X-10096159-C-T",
"variation": {
"id": "ga4gh:VA.DUkul2F3qkeuTZjaqpBGrEZvHeMmtl9u",
"type": "Allele",
"digest": "DUkul2F3qkeuTZjaqpBGrEZvHeMmtl9u",
"location": {
"id": "ga4gh:SL.AUzbNTAwItbwxa8Y38qO4hKoi90JIxpe",
"type": "SequenceLocation",
"digest": "AUzbNTAwItbwxa8Y38qO4hKoi90JIxpe",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP"
},
"start": 10128118,
"end": 10128119,
"sequence": "C"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "T"
}
}
}

Steps to reproduce

1. start docker version of variation normalizer
2. look at this result: http://localhost:8001/variation/normalize?q=X-10096159-C-T&hgvs_dup_del_mode=default&input_assembly=GRCh37

Expected behavior

I expected an output similar to this:

http://localhost:8001/variation/normalize?q=X-2408485-G-C&hgvs_dup_del_mode=default&input_assembly=GRCh37

{
"warnings": [],
"service_meta_": {
"name": "variation-normalizer",
"version": "0.15.0",
"response_datetime": "2025-07-28T18:01:56.378889Z",
"url": "https://github.com/cancervariants/variation-normalization"
},
"variation_query": "X-2408485-G-C",
"variation": {
"id": "ga4gh:VA.qfCjIGMvFCqihesmghZ3ePddcHE5ubNP",
"type": "Allele",
"extensions": [
{
"name": "mane_genes",
"value": [
{
"ncbi_gene_id": 9189,
"hgnc_id": 447,
"symbol": "ZBED1",
"status": [
"mane_select"
]
},
{
"ncbi_gene_id": 207063,
"hgnc_id": 18399,
"symbol": "DHRSX",
"status": [
"mane_select"
]
}
]
}
],
"digest": "qfCjIGMvFCqihesmghZ3ePddcHE5ubNP",
"location": {
"id": "ga4gh:SL.7qxpyQ5-ZWAY83malJHkfl5KZAlplxQt",
"type": "SequenceLocation",
"digest": "7qxpyQ5-ZWAY83malJHkfl5KZAlplxQt",
"sequenceReference": {
"type": "SequenceReference",
"refgetAccession": "SQ.w0WZEvgJF0zf_P4yyTzjjv9oW1z61HHP"
},
"start": 2490443,
"end": 2490444,
"sequence": "G"
},
"state": {
"type": "LiteralSequenceExpression",
"sequence": "C"
}
}
}

Current behavior

Described above

Possible reason(s)

No response

Suggested fix

No response

Branch, commit, and/or version

I'm not sure. Please let me know how I can find this, if necessary.

Screenshots

No response

Environment details

OS sequoia 15.5.

Additional details

No response

Contribution

None

[korikuzma]

@hmcostello @mcannon068nw is this blocking? Are we able to skip these instances?

[hmcostello]

We can skip them, it's just a verification step. Just wanted to let you know of the issue.