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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: 1-16991787-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=16991787&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 16991787,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_022089.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2198C>T",
"hgvs_p": "p.Thr733Met",
"transcript": "NM_022089.4",
"protein_id": "NP_071372.1",
"transcript_support_level": null,
"aa_start": 733,
"aa_end": null,
"aa_length": 1180,
"cds_start": 2198,
"cds_end": null,
"cds_length": 3543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000326735.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022089.4"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2198C>T",
"hgvs_p": "p.Thr733Met",
"transcript": "ENST00000326735.13",
"protein_id": "ENSP00000327214.8",
"transcript_support_level": 1,
"aa_start": 733,
"aa_end": null,
"aa_length": 1180,
"cds_start": 2198,
"cds_end": null,
"cds_length": 3543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022089.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000326735.13"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2183C>T",
"hgvs_p": "p.Thr728Met",
"transcript": "ENST00000452699.5",
"protein_id": "ENSP00000413307.1",
"transcript_support_level": 1,
"aa_start": 728,
"aa_end": null,
"aa_length": 1175,
"cds_start": 2183,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452699.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2183C>T",
"hgvs_p": "p.Thr728Met",
"transcript": "ENST00000341676.9",
"protein_id": "ENSP00000341115.5",
"transcript_support_level": 1,
"aa_start": 728,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2183,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000341676.9"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2183C>T",
"hgvs_p": "p.Thr728Met",
"transcript": "NM_001141973.3",
"protein_id": "NP_001135445.1",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 1175,
"cds_start": 2183,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001141973.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2183C>T",
"hgvs_p": "p.Thr728Met",
"transcript": "NM_001141974.3",
"protein_id": "NP_001135446.1",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2183,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001141974.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.608C>T",
"hgvs_p": "p.Thr203Met",
"transcript": "ENST00000503552.1",
"protein_id": "ENSP00000421126.1",
"transcript_support_level": 5,
"aa_start": 203,
"aa_end": null,
"aa_length": 257,
"cds_start": 608,
"cds_end": null,
"cds_length": 774,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503552.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2195C>T",
"hgvs_p": "p.Thr732Met",
"transcript": "XM_005245810.2",
"protein_id": "XP_005245867.1",
"transcript_support_level": null,
"aa_start": 732,
"aa_end": null,
"aa_length": 1201,
"cds_start": 2195,
"cds_end": null,
"cds_length": 3606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245810.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2183C>T",
"hgvs_p": "p.Thr728Met",
"transcript": "XM_005245811.2",
"protein_id": "XP_005245868.1",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 1197,
"cds_start": 2183,
"cds_end": null,
"cds_length": 3594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245811.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2183C>T",
"hgvs_p": "p.Thr728Met",
"transcript": "XM_011541128.2",
"protein_id": "XP_011539430.1",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 1197,
"cds_start": 2183,
"cds_end": null,
"cds_length": 3594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011541128.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2180C>T",
"hgvs_p": "p.Thr727Met",
"transcript": "XM_006710512.2",
"protein_id": "XP_006710575.1",
"transcript_support_level": null,
"aa_start": 727,
"aa_end": null,
"aa_length": 1196,
"cds_start": 2180,
"cds_end": null,
"cds_length": 3591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006710512.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2180C>T",
"hgvs_p": "p.Thr727Met",
"transcript": "XM_047416537.1",
"protein_id": "XP_047272493.1",
"transcript_support_level": null,
"aa_start": 727,
"aa_end": null,
"aa_length": 1196,
"cds_start": 2180,
"cds_end": null,
"cds_length": 3591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416537.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2171C>T",
"hgvs_p": "p.Thr724Met",
"transcript": "XM_005245812.2",
"protein_id": "XP_005245869.1",
"transcript_support_level": null,
"aa_start": 724,
"aa_end": null,
"aa_length": 1193,
"cds_start": 2171,
"cds_end": null,
"cds_length": 3582,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005245812.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2168C>T",
"hgvs_p": "p.Thr723Met",
"transcript": "XM_047416538.1",
"protein_id": "XP_047272494.1",
"transcript_support_level": null,
"aa_start": 723,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2168,
"cds_end": null,
"cds_length": 3579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416538.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2168C>T",
"hgvs_p": "p.Thr723Met",
"transcript": "XM_047416539.1",
"protein_id": "XP_047272495.1",
"transcript_support_level": null,
"aa_start": 723,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2168,
"cds_end": null,
"cds_length": 3579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416539.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2156C>T",
"hgvs_p": "p.Thr719Met",
"transcript": "XM_006710513.2",
"protein_id": "XP_006710576.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 1188,
"cds_start": 2156,
"cds_end": null,
"cds_length": 3567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006710513.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2153C>T",
"hgvs_p": "p.Thr718Met",
"transcript": "XM_047416542.1",
"protein_id": "XP_047272498.1",
"transcript_support_level": null,
"aa_start": 718,
"aa_end": null,
"aa_length": 1187,
"cds_start": 2153,
"cds_end": null,
"cds_length": 3564,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416542.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2195C>T",
"hgvs_p": "p.Thr732Met",
"transcript": "XM_047416544.1",
"protein_id": "XP_047272500.1",
"transcript_support_level": null,
"aa_start": 732,
"aa_end": null,
"aa_length": 1179,
"cds_start": 2195,
"cds_end": null,
"cds_length": 3540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416544.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2183C>T",
"hgvs_p": "p.Thr728Met",
"transcript": "XM_017000844.2",
"protein_id": "XP_016856333.1",
"transcript_support_level": null,
"aa_start": 728,
"aa_end": null,
"aa_length": 1175,
"cds_start": 2183,
"cds_end": null,
"cds_length": 3528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000844.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2180C>T",
"hgvs_p": "p.Thr727Met",
"transcript": "XM_017000845.2",
"protein_id": "XP_016856334.1",
"transcript_support_level": null,
"aa_start": 727,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2180,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017000845.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2180C>T",
"hgvs_p": "p.Thr727Met",
"transcript": "XM_047416546.1",
"protein_id": "XP_047272502.1",
"transcript_support_level": null,
"aa_start": 727,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2180,
"cds_end": null,
"cds_length": 3525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416546.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2171C>T",
"hgvs_p": "p.Thr724Met",
"transcript": "XM_047416547.1",
"protein_id": "XP_047272503.1",
"transcript_support_level": null,
"aa_start": 724,
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{
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{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
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"exon_count": 28,
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"gene_symbol": "ATP13A2",
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"hgvs_c": "c.1949C>T",
"hgvs_p": "p.Thr650Met",
"transcript": "XM_047416571.1",
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{
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"consequences": [
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],
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"gene_symbol": "ATP13A2",
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{
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],
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"gene_symbol": "ENSG00000226526",
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"biotype": "pseudogene",
"feature": "ENST00000446261.1"
}
],
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"dbsnp": "rs201883464",
"frequency_reference_population": 0.0001331944,
"hom_count_reference_population": 2,
"allele_count_reference_population": 215,
"gnomad_exomes_af": 0.000108767,
"gnomad_genomes_af": 0.000367584,
"gnomad_exomes_ac": 159,
"gnomad_genomes_ac": 56,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.007110267877578735,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.148,
"revel_prediction": "Benign",
"alphamissense_score": 0.0716,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.931,
"phylop100way_prediction": "Benign",
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_022089.4",
"gene_symbol": "ATP13A2",
"hgnc_id": 30213,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2198C>T",
"hgvs_p": "p.Thr733Met"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000446261.1",
"gene_symbol": "ENSG00000226526",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.187+12675G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive spastic paraplegia type 78,Inborn genetic diseases,Kufor-Rakeb syndrome,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:1",
"phenotype_combined": "not provided|Autosomal recessive spastic paraplegia type 78;Kufor-Rakeb syndrome|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}