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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-55479572-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=55479572&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 55479572,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000264634.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.141-8C>T",
"hgvs_p": null,
"transcript": "NM_003392.7",
"protein_id": "NP_003383.4",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 380,
"cds_start": -4,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5841,
"mane_select": "ENST00000264634.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.141-8C>T",
"hgvs_p": null,
"transcript": "ENST00000264634.9",
"protein_id": "ENSP00000264634.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 380,
"cds_start": -4,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5841,
"mane_select": "NM_003392.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.141-8C>T",
"hgvs_p": null,
"transcript": "ENST00000474267.5",
"protein_id": "ENSP00000417310.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 380,
"cds_start": -4,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6042,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "NM_001256105.1",
"protein_id": "NP_001243034.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5582,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "NM_001377271.1",
"protein_id": "NP_001364200.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "NM_001377272.1",
"protein_id": "NP_001364201.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "ENST00000497027.5",
"protein_id": "ENSP00000420104.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "ENST00000482079.1",
"protein_id": "ENSP00000418184.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 213,
"cds_start": -4,
"cds_end": null,
"cds_length": 642,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 959,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "n.137-8C>T",
"hgvs_p": null,
"transcript": "ENST00000497817.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.183-8C>T",
"hgvs_p": null,
"transcript": "XM_017007127.2",
"protein_id": "XP_016862616.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 394,
"cds_start": -4,
"cds_end": null,
"cds_length": 1185,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5664,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_011534086.3",
"protein_id": "XP_011532388.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_011534088.3",
"protein_id": "XP_011532390.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 6252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_011534089.2",
"protein_id": "XP_011532391.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_017007128.2",
"protein_id": "XP_016862617.1",
"transcript_support_level": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448852.1",
"protein_id": "XP_047304808.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
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"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448853.1",
"protein_id": "XP_047304809.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448854.1",
"protein_id": "XP_047304810.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 9914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448855.1",
"protein_id": "XP_047304811.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
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"cdna_start": null,
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"cdna_length": 9613,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448856.1",
"protein_id": "XP_047304812.1",
"transcript_support_level": null,
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"cdna_start": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448857.1",
"protein_id": "XP_047304813.1",
"transcript_support_level": null,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
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"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448858.1",
"protein_id": "XP_047304814.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
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"cds_length": 1098,
"cdna_start": null,
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"cdna_length": 9396,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448859.1",
"protein_id": "XP_047304815.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
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"cdna_start": null,
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"cdna_length": 11371,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448860.1",
"protein_id": "XP_047304816.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 11109,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448861.1",
"protein_id": "XP_047304817.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10433,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"hgvs_c": "c.96-8C>T",
"hgvs_p": null,
"transcript": "XM_047448862.1",
"protein_id": "XP_047304818.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 365,
"cds_start": -4,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "WNT5A",
"gene_hgnc_id": 12784,
"dbsnp": "rs188798140",
"frequency_reference_population": 0.000024205918,
"hom_count_reference_population": 0,
"allele_count_reference_population": 38,
"gnomad_exomes_af": 0.0000204571,
"gnomad_genomes_af": 0.0000591071,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 9,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7799999713897705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.78,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.335,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000139422183880324,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000264634.9",
"gene_symbol": "WNT5A",
"hgnc_id": 12784,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.141-8C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}