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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: 1-21729761-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=21729761&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 21729761,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000308271.14",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "NM_032236.8",
"protein_id": "NP_115612.4",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 1035,
"cds_start": 1243,
"cds_end": null,
"cds_length": 3108,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 4419,
"mane_select": "ENST00000308271.14",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "ENST00000308271.14",
"protein_id": "ENSP00000309262.9",
"transcript_support_level": 1,
"aa_start": 415,
"aa_end": null,
"aa_length": 1035,
"cds_start": 1243,
"cds_end": null,
"cds_length": 3108,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 4419,
"mane_select": "NM_032236.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1240A>G",
"hgvs_p": "p.Met414Val",
"transcript": "ENST00000529637.5",
"protein_id": "ENSP00000431949.1",
"transcript_support_level": 1,
"aa_start": 414,
"aa_end": null,
"aa_length": 1047,
"cds_start": 1240,
"cds_end": null,
"cds_length": 3144,
"cdna_start": 1274,
"cdna_end": null,
"cdna_length": 3228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "ENST00000400301.5",
"protein_id": "ENSP00000383157.1",
"transcript_support_level": 1,
"aa_start": 415,
"aa_end": null,
"aa_length": 983,
"cds_start": 1243,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 1481,
"cdna_end": null,
"cdna_length": 4309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000526044.5",
"protein_id": "ENSP00000431832.1",
"transcript_support_level": 3,
"aa_start": 1,
"aa_end": null,
"aa_length": 134,
"cds_start": 1,
"cds_end": null,
"cds_length": 406,
"cdna_start": 144,
"cdna_end": null,
"cdna_length": 549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_011542267.4",
"protein_id": "XP_011540569.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 621,
"cds_start": 1,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 170,
"cdna_end": null,
"cdna_length": 3154,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"start_lost"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1A>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_011542268.3",
"protein_id": "XP_011540570.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 621,
"cds_start": 1,
"cds_end": null,
"cds_length": 1866,
"cdna_start": 94,
"cdna_end": null,
"cdna_length": 3078,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1240A>G",
"hgvs_p": "p.Met414Val",
"transcript": "NM_001350167.2",
"protein_id": "NP_001337096.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1034,
"cds_start": 1240,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 4416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "NM_001350168.2",
"protein_id": "NP_001337097.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 1034,
"cds_start": 1243,
"cds_end": null,
"cds_length": 3105,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 4416,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1240A>G",
"hgvs_p": "p.Met414Val",
"transcript": "NM_001350166.2",
"protein_id": "NP_001337095.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 1033,
"cds_start": 1240,
"cds_end": null,
"cds_length": 3102,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 4413,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "NM_001330394.3",
"protein_id": "NP_001317323.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 983,
"cds_start": 1243,
"cds_end": null,
"cds_length": 2952,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 4263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1240A>G",
"hgvs_p": "p.Met414Val",
"transcript": "NM_001350164.2",
"protein_id": "NP_001337093.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
"aa_length": 968,
"cds_start": 1240,
"cds_end": null,
"cds_length": 2907,
"cdna_start": 1432,
"cdna_end": null,
"cdna_length": 4218,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "NM_001032730.3",
"protein_id": "NP_001027902.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 485,
"cds_start": 1243,
"cds_end": null,
"cds_length": 1458,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 2361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "ENST00000421625.6",
"protein_id": "ENSP00000406256.2",
"transcript_support_level": 2,
"aa_start": 415,
"aa_end": null,
"aa_length": 485,
"cds_start": 1243,
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"cdna_start": 1892,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.109A>G",
"hgvs_p": "p.Met37Val",
"transcript": "ENST00000534705.5",
"protein_id": "ENSP00000435604.1",
"transcript_support_level": 4,
"aa_start": 37,
"aa_end": null,
"aa_length": 145,
"cds_start": 109,
"cds_end": null,
"cds_length": 440,
"cdna_start": 235,
"cdna_end": null,
"cdna_length": 566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1240A>G",
"hgvs_p": "p.Met414Val",
"transcript": "XM_047432026.1",
"protein_id": "XP_047287982.1",
"transcript_support_level": null,
"aa_start": 414,
"aa_end": null,
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"cdna_start": 1432,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "XM_047432027.1",
"protein_id": "XP_047287983.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 982,
"cds_start": 1243,
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"cds_length": 2949,
"cdna_start": 1435,
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"cdna_length": 4260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "XM_006710955.5",
"protein_id": "XP_006711018.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 969,
"cds_start": 1243,
"cds_end": null,
"cds_length": 2910,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 4221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1042A>G",
"hgvs_p": "p.Met348Val",
"transcript": "XM_011542264.2",
"protein_id": "XP_011540566.1",
"transcript_support_level": null,
"aa_start": 348,
"aa_end": null,
"aa_length": 968,
"cds_start": 1042,
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"cdna_start": 1075,
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"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "XM_047432029.1",
"protein_id": "XP_047287985.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 968,
"cds_start": 1243,
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"cdna_start": 1435,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1240A>G",
"hgvs_p": "p.Met414Val",
"transcript": "XM_047432030.1",
"protein_id": "XP_047287986.1",
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"aa_start": 414,
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"aa_length": 967,
"cds_start": 1240,
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"cdna_start": 1432,
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"cdna_length": 4215,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "XM_047432031.1",
"protein_id": "XP_047287987.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 917,
"cds_start": 1243,
"cds_end": null,
"cds_length": 2754,
"cdna_start": 1435,
"cdna_end": null,
"cdna_length": 4065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "XM_047432032.1",
"protein_id": "XP_047287988.1",
"transcript_support_level": null,
"aa_start": 415,
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"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
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"exon_count": 20,
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"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val",
"transcript": "XM_047432033.1",
"protein_id": "XP_047287989.1",
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"aa_start": 415,
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"cds_length": 2400,
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"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
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"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "n.*59A>G",
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"transcript": "ENST00000374730.2",
"protein_id": "ENSP00000363862.2",
"transcript_support_level": 4,
"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": 570,
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"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
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"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"hgvs_c": "n.*59A>G",
"hgvs_p": null,
"transcript": "ENST00000374730.2",
"protein_id": "ENSP00000363862.2",
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"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": 570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USP48",
"gene_hgnc_id": 18533,
"dbsnp": "rs193921025",
"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": 0.8094683885574341,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.559,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9729,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.459,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000308271.14",
"gene_symbol": "USP48",
"hgnc_id": 18533,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.1243A>G",
"hgvs_p": "p.Met415Val"
}
],
"clinvar_disease": "Prostate cancer",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Prostate cancer",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}