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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: 19-12899466-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=12899466&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 12899466,
"ref": "A",
"alt": "C",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "ENST00000222214.10",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1244-2A>C",
"hgvs_p": null,
"transcript": "NM_000159.4",
"protein_id": "NP_000150.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 438,
"cds_start": -4,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": "ENST00000222214.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1244-2A>C",
"hgvs_p": null,
"transcript": "ENST00000222214.10",
"protein_id": "ENSP00000222214.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 438,
"cds_start": -4,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": "NM_000159.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYCE2",
"gene_hgnc_id": 27411,
"hgvs_c": "c.613-81T>G",
"hgvs_p": null,
"transcript": "NM_001105578.2",
"protein_id": "NP_001099048.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": -4,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1248,
"mane_select": "ENST00000293695.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYCE2",
"gene_hgnc_id": 27411,
"hgvs_c": "c.613-81T>G",
"hgvs_p": null,
"transcript": "ENST00000293695.8",
"protein_id": "ENSP00000293695.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": -4,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1248,
"mane_select": "NM_001105578.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1244-2A>C",
"hgvs_p": null,
"transcript": "ENST00000591470.5",
"protein_id": "ENSP00000466845.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 438,
"cds_start": -4,
"cds_end": null,
"cds_length": 1317,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1867,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1603A>C",
"hgvs_p": null,
"transcript": "ENST00000714069.1",
"protein_id": "ENSP00000519360.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 522,
"cds_start": -4,
"cds_end": null,
"cds_length": 1569,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1603A>C",
"hgvs_p": null,
"transcript": "ENST00000714068.1",
"protein_id": "ENSP00000519359.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 480,
"cds_start": -4,
"cds_end": null,
"cds_length": 1443,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1292-2A>C",
"hgvs_p": null,
"transcript": "ENST00000587072.2",
"protein_id": "ENSP00000468584.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 454,
"cds_start": -4,
"cds_end": null,
"cds_length": 1365,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1603A>C",
"hgvs_p": null,
"transcript": "ENST00000591050.2",
"protein_id": "ENSP00000467735.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 446,
"cds_start": -4,
"cds_end": null,
"cds_length": 1341,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1243+1603A>C",
"hgvs_p": null,
"transcript": "ENST00000714070.1",
"protein_id": "ENSP00000519361.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 439,
"cds_start": -4,
"cds_end": null,
"cds_length": 1320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1217-2A>C",
"hgvs_p": null,
"transcript": "ENST00000714075.1",
"protein_id": "ENSP00000519366.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 429,
"cds_start": -4,
"cds_end": null,
"cds_length": 1290,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1771,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1244-234A>C",
"hgvs_p": null,
"transcript": "NM_013976.5",
"protein_id": "NP_039663.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 428,
"cds_start": -4,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1244-234A>C",
"hgvs_p": null,
"transcript": "ENST00000714073.1",
"protein_id": "ENSP00000519364.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 428,
"cds_start": -4,
"cds_end": null,
"cds_length": 1287,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1208-2A>C",
"hgvs_p": null,
"transcript": "ENST00000588905.6",
"protein_id": "ENSP00000465770.2",
"transcript_support_level": 5,
"aa_start": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "c.1118-2A>C",
"hgvs_p": null,
"transcript": "ENST00000714072.1",
"protein_id": "ENSP00000519363.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 396,
"cds_start": -4,
"cds_end": null,
"cds_length": 1191,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1414,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SYCE2",
"gene_hgnc_id": 27411,
"hgvs_c": "c.*23-81T>G",
"hgvs_p": null,
"transcript": "ENST00000592819.1",
"protein_id": "ENSP00000466359.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
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"cds_start": -4,
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"cdna_start": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1574-2A>C",
"hgvs_p": null,
"transcript": "ENST00000585420.5",
"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,
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"cdna_length": 1730,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.*735-2A>C",
"hgvs_p": null,
"transcript": "ENST00000589039.6",
"protein_id": "ENSP00000465618.1",
"transcript_support_level": 5,
"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": 1789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.*684-2A>C",
"hgvs_p": null,
"transcript": "ENST00000590530.5",
"protein_id": "ENSP00000468452.1",
"transcript_support_level": 2,
"aa_start": null,
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"aa_length": 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": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1554-2A>C",
"hgvs_p": null,
"transcript": "ENST00000591043.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"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,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1244-2A>C",
"hgvs_p": null,
"transcript": "ENST00000714074.1",
"protein_id": "ENSP00000519365.1",
"transcript_support_level": null,
"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": 3178,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1407-2A>C",
"hgvs_p": null,
"transcript": "NR_102316.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.1625-2A>C",
"hgvs_p": null,
"transcript": "NR_102317.1",
"protein_id": null,
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"cds_start": -4,
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},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": true,
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"consequences": [
"intron_variant"
],
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"exon_count": 6,
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"gene_symbol": "SYCE2",
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"hgvs_c": "c.610-81T>G",
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"transcript": "XM_011527882.3",
"protein_id": "XP_011526184.1",
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},
{
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"canonical": false,
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"strand": true,
"consequences": [
"upstream_gene_variant"
],
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"exon_count": 2,
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"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"hgvs_c": "n.-105A>C",
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"transcript": "ENST00000588242.2",
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"cdna_length": 1006,
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}
],
"gene_symbol": "GCDH",
"gene_hgnc_id": 4189,
"dbsnp": "rs199999619",
"frequency_reference_population": 0.000013009428,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000109448,
"gnomad_genomes_af": 0.0000328226,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3499999940395355,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9279999732971191,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.062,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.91,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999988247793601,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000222214.10",
"gene_symbol": "GCDH",
"hgnc_id": 4189,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1244-2A>C",
"hgvs_p": null
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000293695.8",
"gene_symbol": "SYCE2",
"hgnc_id": 27411,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.613-81T>G",
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}
],
"clinvar_disease": " type 1,Glutaric aciduria,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:9",
"phenotype_combined": "Glutaric aciduria, type 1|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}