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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: 3-169100904-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=169100904&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 169100904,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000651503.2",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Thr944Ala",
"transcript": "NM_004991.4",
"protein_id": "NP_004982.2",
"transcript_support_level": null,
"aa_start": 944,
"aa_end": null,
"aa_length": 1239,
"cds_start": 2830,
"cds_end": null,
"cds_length": 3720,
"cdna_start": 3170,
"cdna_end": null,
"cdna_length": 5462,
"mane_select": "ENST00000651503.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Thr944Ala",
"transcript": "ENST00000651503.2",
"protein_id": "ENSP00000498411.1",
"transcript_support_level": null,
"aa_start": 944,
"aa_end": null,
"aa_length": 1239,
"cds_start": 2830,
"cds_end": null,
"cds_length": 3720,
"cdna_start": 3170,
"cdna_end": null,
"cdna_length": 5462,
"mane_select": "NM_004991.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2461A>G",
"hgvs_p": "p.Thr821Ala",
"transcript": "ENST00000264674.7",
"protein_id": "ENSP00000264674.3",
"transcript_support_level": 1,
"aa_start": 821,
"aa_end": null,
"aa_length": 1116,
"cds_start": 2461,
"cds_end": null,
"cds_length": 3351,
"cdna_start": 2600,
"cdna_end": null,
"cdna_length": 4900,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2269A>G",
"hgvs_p": "p.Thr757Ala",
"transcript": "ENST00000433243.6",
"protein_id": "ENSP00000394302.2",
"transcript_support_level": 1,
"aa_start": 757,
"aa_end": null,
"aa_length": 1052,
"cds_start": 2269,
"cds_end": null,
"cds_length": 3159,
"cdna_start": 2583,
"cdna_end": null,
"cdna_length": 3508,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2266A>G",
"hgvs_p": "p.Thr756Ala",
"transcript": "ENST00000628990.2",
"protein_id": "ENSP00000486104.1",
"transcript_support_level": 1,
"aa_start": 756,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2266,
"cds_end": null,
"cds_length": 3156,
"cdna_start": 2535,
"cdna_end": null,
"cdna_length": 4835,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2239A>G",
"hgvs_p": "p.Thr747Ala",
"transcript": "ENST00000464456.5",
"protein_id": "ENSP00000419770.1",
"transcript_support_level": 1,
"aa_start": 747,
"aa_end": null,
"aa_length": 1042,
"cds_start": 2239,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 3440,
"cdna_end": null,
"cdna_length": 5732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2239A>G",
"hgvs_p": "p.Thr747Ala",
"transcript": "ENST00000460814.5",
"protein_id": "ENSP00000420466.1",
"transcript_support_level": 1,
"aa_start": 747,
"aa_end": null,
"aa_length": 1003,
"cds_start": 2239,
"cds_end": null,
"cds_length": 3012,
"cdna_start": 2352,
"cdna_end": null,
"cdna_length": 3374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2803A>G",
"hgvs_p": "p.Thr935Ala",
"transcript": "NM_001366466.2",
"protein_id": "NP_001353395.1",
"transcript_support_level": null,
"aa_start": 935,
"aa_end": null,
"aa_length": 1230,
"cds_start": 2803,
"cds_end": null,
"cds_length": 3693,
"cdna_start": 3143,
"cdna_end": null,
"cdna_length": 5435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2803A>G",
"hgvs_p": "p.Thr935Ala",
"transcript": "ENST00000494292.6",
"protein_id": "ENSP00000417899.1",
"transcript_support_level": 5,
"aa_start": 935,
"aa_end": null,
"aa_length": 1230,
"cds_start": 2803,
"cds_end": null,
"cds_length": 3693,
"cdna_start": 3206,
"cdna_end": null,
"cdna_length": 4244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2461A>G",
"hgvs_p": "p.Thr821Ala",
"transcript": "NM_001105077.4",
"protein_id": "NP_001098547.3",
"transcript_support_level": null,
"aa_start": 821,
"aa_end": null,
"aa_length": 1116,
"cds_start": 2461,
"cds_end": null,
"cds_length": 3351,
"cdna_start": 2600,
"cdna_end": null,
"cdna_length": 4892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2269A>G",
"hgvs_p": "p.Thr757Ala",
"transcript": "NM_001366467.2",
"protein_id": "NP_001353396.1",
"transcript_support_level": null,
"aa_start": 757,
"aa_end": null,
"aa_length": 1052,
"cds_start": 2269,
"cds_end": null,
"cds_length": 3159,
"cdna_start": 3207,
"cdna_end": null,
"cdna_length": 5499,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2269A>G",
"hgvs_p": "p.Thr757Ala",
"transcript": "NM_001366468.2",
"protein_id": "NP_001353397.1",
"transcript_support_level": null,
"aa_start": 757,
"aa_end": null,
"aa_length": 1052,
"cds_start": 2269,
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"cds_length": 3159,
"cdna_start": 2521,
"cdna_end": null,
"cdna_length": 4813,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2269A>G",
"hgvs_p": "p.Thr757Ala",
"transcript": "ENST00000472280.5",
"protein_id": "ENSP00000420048.1",
"transcript_support_level": 5,
"aa_start": 757,
"aa_end": null,
"aa_length": 1052,
"cds_start": 2269,
"cds_end": null,
"cds_length": 3159,
"cdna_start": 2538,
"cdna_end": null,
"cdna_length": 3593,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2266A>G",
"hgvs_p": "p.Thr756Ala",
"transcript": "NM_001105078.4",
"protein_id": "NP_001098548.2",
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"aa_start": 756,
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"cdna_start": 2518,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2266A>G",
"hgvs_p": "p.Thr756Ala",
"transcript": "NM_001205194.2",
"protein_id": "NP_001192123.1",
"transcript_support_level": null,
"aa_start": 756,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2266,
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"cdna_start": 2832,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2266A>G",
"hgvs_p": "p.Thr756Ala",
"transcript": "NM_001366469.2",
"protein_id": "NP_001353398.1",
"transcript_support_level": null,
"aa_start": 756,
"aa_end": null,
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"cdna_start": 3204,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2266A>G",
"hgvs_p": "p.Thr756Ala",
"transcript": "NM_005241.4",
"protein_id": "NP_005232.2",
"transcript_support_level": null,
"aa_start": 756,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2266,
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"cdna_start": 2535,
"cdna_end": null,
"cdna_length": 4827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2266A>G",
"hgvs_p": "p.Thr756Ala",
"transcript": "ENST00000468789.5",
"protein_id": "ENSP00000419995.1",
"transcript_support_level": 2,
"aa_start": 756,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2266,
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"cdna_start": 2654,
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"cdna_length": 3691,
"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2242A>G",
"hgvs_p": "p.Thr748Ala",
"transcript": "NM_001163999.2",
"protein_id": "NP_001157471.1",
"transcript_support_level": null,
"aa_start": 748,
"aa_end": null,
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"mane_plus": null,
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"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2242A>G",
"hgvs_p": "p.Thr748Ala",
"transcript": "NM_001366470.2",
"protein_id": "NP_001353399.1",
"transcript_support_level": null,
"aa_start": 748,
"aa_end": null,
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"cds_start": 2242,
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"cdna_start": 3180,
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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": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2239A>G",
"hgvs_p": "p.Thr747Ala",
"transcript": "NM_001164000.2",
"protein_id": "NP_001157472.1",
"transcript_support_level": null,
"aa_start": 747,
"aa_end": null,
"aa_length": 1042,
"cds_start": 2239,
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"cds_length": 3129,
"cdna_start": 3177,
"cdna_end": null,
"cdna_length": 5469,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.2239A>G",
"hgvs_p": "p.Thr747Ala",
"transcript": "NM_001366471.2",
"protein_id": "NP_001353400.1",
"transcript_support_level": null,
"aa_start": 747,
"aa_end": null,
"aa_length": 1042,
"cds_start": 2239,
"cds_end": null,
"cds_length": 3129,
"cdna_start": 2491,
"cdna_end": null,
"cdna_length": 4783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
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"cds_end": null,
"cds_length": 2160,
"cdna_start": 1522,
"cdna_end": null,
"cdna_length": 3814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"hgvs_c": "c.1267A>G",
"hgvs_p": "p.Thr423Ala",
"transcript": "XM_047447694.1",
"protein_id": "XP_047303650.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 718,
"cds_start": 1267,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 1519,
"cdna_end": null,
"cdna_length": 3811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MECOM",
"gene_hgnc_id": 3498,
"dbsnp": "rs864309722",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7968255281448364,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.515,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9773,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 8.017,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3,PP5",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000651503.2",
"gene_symbol": "MECOM",
"hgnc_id": 3498,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2830A>G",
"hgvs_p": "p.Thr944Ala"
}
],
"clinvar_disease": "Radioulnar synostosis with amegakaryocytic thrombocytopenia 2",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Radioulnar synostosis with amegakaryocytic thrombocytopenia 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}