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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: 3-9371316-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=9371316&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 9371316,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_015453.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "NM_001114092.2",
"protein_id": "NP_001107564.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 714,
"cdna_end": null,
"cdna_length": 3754,
"mane_select": "ENST00000452837.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001114092.2"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000452837.7",
"protein_id": "ENSP00000395893.2",
"transcript_support_level": 1,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 714,
"cdna_end": null,
"cdna_length": 3754,
"mane_select": "NM_001114092.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000452837.7"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000515662.6",
"protein_id": "ENSP00000424064.1",
"transcript_support_level": 1,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1271,
"cdna_end": null,
"cdna_length": 2390,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000515662.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "THUMPD3-AS1",
"gene_hgnc_id": 44478,
"hgvs_c": "n.2875+18974T>A",
"hgvs_p": null,
"transcript": "ENST00000468186.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3253,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000468186.5"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.593A>T",
"hgvs_p": "p.Asp198Val",
"transcript": "ENST00000912100.1",
"protein_id": "ENSP00000582159.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 509,
"cds_start": 593,
"cds_end": null,
"cds_length": 1530,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 1746,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912100.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "NM_015453.3",
"protein_id": "NP_056268.2",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 919,
"cdna_end": null,
"cdna_length": 3959,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015453.3"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000345094.7",
"protein_id": "ENSP00000339532.3",
"transcript_support_level": 2,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 921,
"cdna_end": null,
"cdna_length": 3961,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000345094.7"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874843.1",
"protein_id": "ENSP00000544902.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 986,
"cdna_end": null,
"cdna_length": 4023,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874843.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874844.1",
"protein_id": "ENSP00000544903.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 909,
"cdna_end": null,
"cdna_length": 3939,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874844.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874845.1",
"protein_id": "ENSP00000544904.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1366,
"cdna_end": null,
"cdna_length": 4177,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874845.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874846.1",
"protein_id": "ENSP00000544905.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1783,
"cdna_end": null,
"cdna_length": 4588,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874846.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874847.1",
"protein_id": "ENSP00000544906.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 901,
"cdna_end": null,
"cdna_length": 3704,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874847.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874849.1",
"protein_id": "ENSP00000544908.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 758,
"cdna_end": null,
"cdna_length": 2710,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874849.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874850.1",
"protein_id": "ENSP00000544909.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1066,
"cdna_end": null,
"cdna_length": 2187,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874850.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000874851.1",
"protein_id": "ENSP00000544910.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 702,
"cdna_end": null,
"cdna_length": 1740,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000874851.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000912094.1",
"protein_id": "ENSP00000582153.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1079,
"cdna_end": null,
"cdna_length": 3031,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912094.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000912095.1",
"protein_id": "ENSP00000582154.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1322,
"cdna_end": null,
"cdna_length": 3274,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912095.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000912096.1",
"protein_id": "ENSP00000582155.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 832,
"cdna_end": null,
"cdna_length": 2784,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912096.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000912097.1",
"protein_id": "ENSP00000582156.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1170,
"cdna_end": null,
"cdna_length": 2409,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912097.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000912099.1",
"protein_id": "ENSP00000582158.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 1107,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912099.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000951554.1",
"protein_id": "ENSP00000621613.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 922,
"cdna_end": null,
"cdna_length": 3266,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951554.1"
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "THUMPD3",
"gene_hgnc_id": 24493,
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val",
"transcript": "ENST00000951555.1",
"protein_id": "ENSP00000621614.1",
"transcript_support_level": null,
"aa_start": 196,
"aa_end": null,
"aa_length": 507,
"cds_start": 587,
"cds_end": null,
"cds_length": 1524,
"cdna_start": 2597,
"cdna_end": null,
"cdna_length": 4941,
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{
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"strand": true,
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],
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{
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],
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},
{
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],
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},
{
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"strand": true,
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"downstream_gene_variant"
],
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"gene_symbol": "THUMPD3",
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"transcript": "ENST00000419437.5",
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"feature": "ENST00000419437.5"
},
{
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"strand": true,
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"upstream_gene_variant"
],
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"gene_symbol": "THUMPD3",
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"hgvs_c": "n.-138A>T",
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"transcript": "ENST00000461636.1",
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"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000461636.1"
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],
"gene_symbol": "THUMPD3",
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"dbsnp": "rs113156616",
"frequency_reference_population": 0.000063811305,
"hom_count_reference_population": 1,
"allele_count_reference_population": 103,
"gnomad_exomes_af": 0.000055411,
"gnomad_genomes_af": 0.000144423,
"gnomad_exomes_ac": 81,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05037814378738403,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.162,
"revel_prediction": "Benign",
"alphamissense_score": 0.1061,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.294,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_015453.3",
"gene_symbol": "THUMPD3",
"hgnc_id": 24493,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.587A>T",
"hgvs_p": "p.Asp196Val"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000468186.5",
"gene_symbol": "THUMPD3-AS1",
"hgnc_id": 44478,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2875+18974T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}