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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: 1-16987187-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=16987187&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 16987187,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000326735.13",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2942C>T",
"hgvs_p": "p.Thr981Met",
"transcript": "NM_022089.4",
"protein_id": "NP_071372.1",
"transcript_support_level": null,
"aa_start": 981,
"aa_end": null,
"aa_length": 1180,
"cds_start": 2942,
"cds_end": null,
"cds_length": 3543,
"cdna_start": 3132,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": "ENST00000326735.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2942C>T",
"hgvs_p": "p.Thr981Met",
"transcript": "ENST00000326735.13",
"protein_id": "ENSP00000327214.8",
"transcript_support_level": 1,
"aa_start": 981,
"aa_end": null,
"aa_length": 1180,
"cds_start": 2942,
"cds_end": null,
"cds_length": 3543,
"cdna_start": 3132,
"cdna_end": null,
"cdna_length": 3996,
"mane_select": "NM_022089.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2927C>T",
"hgvs_p": "p.Thr976Met",
"transcript": "ENST00000452699.5",
"protein_id": "ENSP00000413307.1",
"transcript_support_level": 1,
"aa_start": 976,
"aa_end": null,
"aa_length": 1175,
"cds_start": 2927,
"cds_end": null,
"cds_length": 3528,
"cdna_start": 3117,
"cdna_end": null,
"cdna_length": 3981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2810C>T",
"hgvs_p": "p.Thr937Met",
"transcript": "ENST00000341676.9",
"protein_id": "ENSP00000341115.5",
"transcript_support_level": 1,
"aa_start": 937,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2810,
"cds_end": null,
"cds_length": 3477,
"cdna_start": 2987,
"cdna_end": null,
"cdna_length": 3681,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2927C>T",
"hgvs_p": "p.Thr976Met",
"transcript": "NM_001141973.3",
"protein_id": "NP_001135445.1",
"transcript_support_level": null,
"aa_start": 976,
"aa_end": null,
"aa_length": 1175,
"cds_start": 2927,
"cds_end": null,
"cds_length": 3528,
"cdna_start": 3117,
"cdna_end": null,
"cdna_length": 3981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2810C>T",
"hgvs_p": "p.Thr937Met",
"transcript": "NM_001141974.3",
"protein_id": "NP_001135446.1",
"transcript_support_level": null,
"aa_start": 937,
"aa_end": null,
"aa_length": 1158,
"cds_start": 2810,
"cds_end": null,
"cds_length": 3477,
"cdna_start": 3000,
"cdna_end": null,
"cdna_length": 3694,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.530C>T",
"hgvs_p": "p.Thr177Met",
"transcript": "ENST00000502418.1",
"protein_id": "ENSP00000423065.1",
"transcript_support_level": 3,
"aa_start": 177,
"aa_end": null,
"aa_length": 398,
"cds_start": 530,
"cds_end": null,
"cds_length": 1197,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 1201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2939C>T",
"hgvs_p": "p.Thr980Met",
"transcript": "XM_005245810.2",
"protein_id": "XP_005245867.1",
"transcript_support_level": null,
"aa_start": 980,
"aa_end": null,
"aa_length": 1201,
"cds_start": 2939,
"cds_end": null,
"cds_length": 3606,
"cdna_start": 3129,
"cdna_end": null,
"cdna_length": 3823,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2927C>T",
"hgvs_p": "p.Thr976Met",
"transcript": "XM_005245811.2",
"protein_id": "XP_005245868.1",
"transcript_support_level": null,
"aa_start": 976,
"aa_end": null,
"aa_length": 1197,
"cds_start": 2927,
"cds_end": null,
"cds_length": 3594,
"cdna_start": 3117,
"cdna_end": null,
"cdna_length": 3811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2927C>T",
"hgvs_p": "p.Thr976Met",
"transcript": "XM_011541128.2",
"protein_id": "XP_011539430.1",
"transcript_support_level": null,
"aa_start": 976,
"aa_end": null,
"aa_length": 1197,
"cds_start": 2927,
"cds_end": null,
"cds_length": 3594,
"cdna_start": 3117,
"cdna_end": null,
"cdna_length": 3811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2924C>T",
"hgvs_p": "p.Thr975Met",
"transcript": "XM_006710512.2",
"protein_id": "XP_006710575.1",
"transcript_support_level": null,
"aa_start": 975,
"aa_end": null,
"aa_length": 1196,
"cds_start": 2924,
"cds_end": null,
"cds_length": 3591,
"cdna_start": 3114,
"cdna_end": null,
"cdna_length": 3808,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2924C>T",
"hgvs_p": "p.Thr975Met",
"transcript": "XM_047416537.1",
"protein_id": "XP_047272493.1",
"transcript_support_level": null,
"aa_start": 975,
"aa_end": null,
"aa_length": 1196,
"cds_start": 2924,
"cds_end": null,
"cds_length": 3591,
"cdna_start": 3114,
"cdna_end": null,
"cdna_length": 3808,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2915C>T",
"hgvs_p": "p.Thr972Met",
"transcript": "XM_005245812.2",
"protein_id": "XP_005245869.1",
"transcript_support_level": null,
"aa_start": 972,
"aa_end": null,
"aa_length": 1193,
"cds_start": 2915,
"cds_end": null,
"cds_length": 3582,
"cdna_start": 3105,
"cdna_end": null,
"cdna_length": 3799,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2912C>T",
"hgvs_p": "p.Thr971Met",
"transcript": "XM_047416538.1",
"protein_id": "XP_047272494.1",
"transcript_support_level": null,
"aa_start": 971,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2912,
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"cdna_start": 3102,
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"cdna_length": 3796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2912C>T",
"hgvs_p": "p.Thr971Met",
"transcript": "XM_047416539.1",
"protein_id": "XP_047272495.1",
"transcript_support_level": null,
"aa_start": 971,
"aa_end": null,
"aa_length": 1192,
"cds_start": 2912,
"cds_end": null,
"cds_length": 3579,
"cdna_start": 3102,
"cdna_end": null,
"cdna_length": 3796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2900C>T",
"hgvs_p": "p.Thr967Met",
"transcript": "XM_006710513.2",
"protein_id": "XP_006710576.1",
"transcript_support_level": null,
"aa_start": 967,
"aa_end": null,
"aa_length": 1188,
"cds_start": 2900,
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"cds_length": 3567,
"cdna_start": 3090,
"cdna_end": null,
"cdna_length": 3784,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2897C>T",
"hgvs_p": "p.Thr966Met",
"transcript": "XM_047416542.1",
"protein_id": "XP_047272498.1",
"transcript_support_level": null,
"aa_start": 966,
"aa_end": null,
"aa_length": 1187,
"cds_start": 2897,
"cds_end": null,
"cds_length": 3564,
"cdna_start": 3087,
"cdna_end": null,
"cdna_length": 3781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2939C>T",
"hgvs_p": "p.Thr980Met",
"transcript": "XM_047416544.1",
"protein_id": "XP_047272500.1",
"transcript_support_level": null,
"aa_start": 980,
"aa_end": null,
"aa_length": 1179,
"cds_start": 2939,
"cds_end": null,
"cds_length": 3540,
"cdna_start": 3129,
"cdna_end": null,
"cdna_length": 3993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2927C>T",
"hgvs_p": "p.Thr976Met",
"transcript": "XM_017000844.2",
"protein_id": "XP_016856333.1",
"transcript_support_level": null,
"aa_start": 976,
"aa_end": null,
"aa_length": 1175,
"cds_start": 2927,
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"cdna_start": 3117,
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"cdna_length": 3981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2924C>T",
"hgvs_p": "p.Thr975Met",
"transcript": "XM_017000845.2",
"protein_id": "XP_016856334.1",
"transcript_support_level": null,
"aa_start": 975,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2924,
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"cdna_start": 3114,
"cdna_end": null,
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"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2924C>T",
"hgvs_p": "p.Thr975Met",
"transcript": "XM_047416546.1",
"protein_id": "XP_047272502.1",
"transcript_support_level": null,
"aa_start": 975,
"aa_end": null,
"aa_length": 1174,
"cds_start": 2924,
"cds_end": null,
"cds_length": 3525,
"cdna_start": 3114,
"cdna_end": null,
"cdna_length": 3978,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"hgvs_c": "c.2915C>T",
"hgvs_p": "p.Thr972Met",
"transcript": "XM_047416547.1",
"protein_id": "XP_047272503.1",
"transcript_support_level": null,
"aa_start": 972,
"aa_end": null,
"aa_length": 1171,
"cds_start": 2915,
"cds_end": null,
"cds_length": 3516,
"cdna_start": 3105,
"cdna_end": null,
"cdna_length": 3969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
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"feature": null
},
{
"aa_ref": "T",
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
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],
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"hgvs_c": "c.2693C>T",
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
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"exon_count": 9,
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"gene_symbol": "ATP13A2",
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"hgvs_c": "n.816C>T",
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"transcript": "ENST00000466561.1",
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"cds_start": -4,
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
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"gene_symbol": "ENSG00000226526",
"gene_hgnc_id": null,
"hgvs_c": "n.187+8075G>A",
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"transcript": "ENST00000446261.1",
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"transcript_support_level": 3,
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"aa_length": null,
"cds_start": -4,
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"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP13A2",
"gene_hgnc_id": 30213,
"dbsnp": "rs148201608",
"frequency_reference_population": 0.00013757085,
"hom_count_reference_population": 0,
"allele_count_reference_population": 222,
"gnomad_exomes_af": 0.0000827973,
"gnomad_genomes_af": 0.000663104,
"gnomad_exomes_ac": 121,
"gnomad_genomes_ac": 101,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.21194279193878174,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.488,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.161,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.088,
"phylop100way_prediction": "Uncertain_significance",
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000326735.13",
"gene_symbol": "ATP13A2",
"hgnc_id": 30213,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2942C>T",
"hgvs_p": "p.Thr981Met"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "ENST00000446261.1",
"gene_symbol": "ENSG00000226526",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.187+8075G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive spastic paraplegia type 78,Inborn genetic diseases,Kufor-Rakeb syndrome",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "Autosomal recessive spastic paraplegia type 78;Kufor-Rakeb syndrome|Inborn genetic diseases",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}