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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: 11-86014944-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=86014944&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 86014944,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000393346.8",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "NM_007166.4",
"protein_id": "NP_009097.2",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 652,
"cds_start": 472,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": "ENST00000393346.8",
"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": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "ENST00000393346.8",
"protein_id": "ENSP00000377015.3",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 652,
"cds_start": 472,
"cds_end": null,
"cds_length": 1959,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 4134,
"mane_select": "NM_007166.4",
"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": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "ENST00000526033.5",
"protein_id": "ENSP00000433846.1",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 645,
"cds_start": 472,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 789,
"cdna_end": null,
"cdna_length": 3613,
"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": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "ENST00000532317.5",
"protein_id": "ENSP00000436958.1",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 610,
"cds_start": 472,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 751,
"cdna_end": null,
"cdna_length": 3474,
"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": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "NM_001206946.2",
"protein_id": "NP_001193875.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 645,
"cds_start": 472,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 4113,
"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": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "NM_001411034.1",
"protein_id": "NP_001397963.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 632,
"cds_start": 472,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 4074,
"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": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "ENST00000356360.9",
"protein_id": "ENSP00000348718.5",
"transcript_support_level": 5,
"aa_start": 158,
"aa_end": null,
"aa_length": 632,
"cds_start": 472,
"cds_end": null,
"cds_length": 1899,
"cdna_start": 472,
"cdna_end": null,
"cdna_length": 1958,
"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": 5,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "NM_001008660.3",
"protein_id": "NP_001008660.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 610,
"cds_start": 472,
"cds_end": null,
"cds_length": 1833,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 4008,
"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": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.319A>G",
"hgvs_p": "p.Thr107Ala",
"transcript": "NM_001206947.2",
"protein_id": "NP_001193876.1",
"transcript_support_level": null,
"aa_start": 107,
"aa_end": null,
"aa_length": 551,
"cds_start": 319,
"cds_end": null,
"cds_length": 1656,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 3691,
"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": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.319A>G",
"hgvs_p": "p.Thr107Ala",
"transcript": "ENST00000528398.5",
"protein_id": "ENSP00000434884.1",
"transcript_support_level": 2,
"aa_start": 107,
"aa_end": null,
"aa_length": 551,
"cds_start": 319,
"cds_end": null,
"cds_length": 1656,
"cdna_start": 505,
"cdna_end": null,
"cdna_length": 2049,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.370A>G",
"hgvs_p": "p.Thr124Ala",
"transcript": "ENST00000531930.5",
"protein_id": "ENSP00000433303.1",
"transcript_support_level": 5,
"aa_start": 124,
"aa_end": null,
"aa_length": 184,
"cds_start": 370,
"cds_end": null,
"cds_length": 556,
"cdna_start": 517,
"cdna_end": null,
"cdna_length": 703,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.370A>G",
"hgvs_p": "p.Thr124Ala",
"transcript": "ENST00000528256.1",
"protein_id": "ENSP00000431545.1",
"transcript_support_level": 4,
"aa_start": 124,
"aa_end": null,
"aa_length": 147,
"cds_start": 370,
"cds_end": null,
"cds_length": 444,
"cdna_start": 489,
"cdna_end": null,
"cdna_length": 563,
"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": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.319A>G",
"hgvs_p": "p.Thr107Ala",
"transcript": "ENST00000525162.5",
"protein_id": "ENSP00000436508.1",
"transcript_support_level": 4,
"aa_start": 107,
"aa_end": null,
"aa_length": 146,
"cds_start": 319,
"cds_end": null,
"cds_length": 443,
"cdna_start": 424,
"cdna_end": null,
"cdna_length": 548,
"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": [
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],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_005274322.4",
"protein_id": "XP_005274379.1",
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"aa_start": 158,
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"biotype": null,
"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 5,
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"exon_count": 21,
"intron_rank": null,
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"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_005274326.4",
"protein_id": "XP_005274383.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 660,
"cds_start": 472,
"cds_end": null,
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"cdna_start": 776,
"cdna_end": null,
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"mane_select": null,
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"biotype": null,
"feature": null
},
{
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"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_005274328.4",
"protein_id": "XP_005274385.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 5,
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"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_024448700.2",
"protein_id": "XP_024304468.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
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"cds_start": 472,
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"cdna_start": 776,
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"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": 5,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_017018381.3",
"protein_id": "XP_016873870.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 648,
"cds_start": 472,
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"cdna_start": 776,
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"mane_select": null,
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"biotype": null,
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},
{
"aa_ref": "T",
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"strand": false,
"consequences": [
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],
"exon_rank": 5,
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"exon_count": 20,
"intron_rank": null,
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"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_005274329.5",
"protein_id": "XP_005274386.1",
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},
{
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"protein_coding": true,
"strand": false,
"consequences": [
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],
"exon_rank": 5,
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"exon_count": 20,
"intron_rank": null,
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"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_047427659.1",
"protein_id": "XP_047283615.1",
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"aa_start": 158,
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"aa_length": 640,
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"feature": null
},
{
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"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
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"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.319A>G",
"hgvs_p": "p.Thr107Ala",
"transcript": "XM_047427660.1",
"protein_id": "XP_047283616.1",
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"cdna_start": 483,
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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": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_005274334.4",
"protein_id": "XP_005274391.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 627,
"cds_start": 472,
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"cds_length": 1884,
"cdna_start": 776,
"cdna_end": null,
"cdna_length": 4059,
"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": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala",
"transcript": "XM_047427661.1",
"protein_id": "XP_047283617.1",
"transcript_support_level": null,
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"hgvs_c": "n.*3A>G",
"hgvs_p": null,
"transcript": "ENST00000534412.5",
"protein_id": "ENSP00000435499.1",
"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": 811,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PICALM",
"gene_hgnc_id": 15514,
"dbsnp": "rs12800974",
"frequency_reference_population": 0.0000065664194,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000656642,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7644174098968506,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.417,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1157,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"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": 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": "ENST00000393346.8",
"gene_symbol": "PICALM",
"hgnc_id": 15514,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.472A>G",
"hgvs_p": "p.Thr158Ala"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}