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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: 4-25748522-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=25748522&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 25748522,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_015187.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3302C>T",
"hgvs_p": "p.Thr1101Ile",
"transcript": "NM_015187.5",
"protein_id": "NP_056002.2",
"transcript_support_level": null,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3302,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3454,
"cdna_end": null,
"cdna_length": 4543,
"mane_select": "ENST00000399878.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015187.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3302C>T",
"hgvs_p": "p.Thr1101Ile",
"transcript": "ENST00000399878.8",
"protein_id": "ENSP00000382767.3",
"transcript_support_level": 1,
"aa_start": 1101,
"aa_end": null,
"aa_length": 1132,
"cds_start": 3302,
"cds_end": null,
"cds_length": 3399,
"cdna_start": 3454,
"cdna_end": null,
"cdna_length": 4543,
"mane_select": "NM_015187.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000399878.8"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3197C>T",
"hgvs_p": "p.Thr1066Ile",
"transcript": "ENST00000264868.9",
"protein_id": "ENSP00000264868.5",
"transcript_support_level": 1,
"aa_start": 1066,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3197,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3280,
"cdna_end": null,
"cdna_length": 4369,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264868.9"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3407C>T",
"hgvs_p": "p.Thr1136Ile",
"transcript": "ENST00000929301.1",
"protein_id": "ENSP00000599360.1",
"transcript_support_level": null,
"aa_start": 1136,
"aa_end": null,
"aa_length": 1167,
"cds_start": 3407,
"cds_end": null,
"cds_length": 3504,
"cdna_start": 3619,
"cdna_end": null,
"cdna_length": 4708,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929301.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3239C>T",
"hgvs_p": "p.Thr1080Ile",
"transcript": "ENST00000929305.1",
"protein_id": "ENSP00000599364.1",
"transcript_support_level": null,
"aa_start": 1080,
"aa_end": null,
"aa_length": 1111,
"cds_start": 3239,
"cds_end": null,
"cds_length": 3336,
"cdna_start": 3252,
"cdna_end": null,
"cdna_length": 4341,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929305.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3218C>T",
"hgvs_p": "p.Thr1073Ile",
"transcript": "ENST00000929304.1",
"protein_id": "ENSP00000599363.1",
"transcript_support_level": null,
"aa_start": 1073,
"aa_end": null,
"aa_length": 1104,
"cds_start": 3218,
"cds_end": null,
"cds_length": 3315,
"cdna_start": 3367,
"cdna_end": null,
"cdna_length": 4456,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929304.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3197C>T",
"hgvs_p": "p.Thr1066Ile",
"transcript": "NM_001297592.2",
"protein_id": "NP_001284521.1",
"transcript_support_level": null,
"aa_start": 1066,
"aa_end": null,
"aa_length": 1097,
"cds_start": 3197,
"cds_end": null,
"cds_length": 3294,
"cdna_start": 3251,
"cdna_end": null,
"cdna_length": 4340,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001297592.2"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3188C>T",
"hgvs_p": "p.Thr1063Ile",
"transcript": "ENST00000960872.1",
"protein_id": "ENSP00000630931.1",
"transcript_support_level": null,
"aa_start": 1063,
"aa_end": null,
"aa_length": 1094,
"cds_start": 3188,
"cds_end": null,
"cds_length": 3285,
"cdna_start": 3190,
"cdna_end": null,
"cdna_length": 4276,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960872.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3122C>T",
"hgvs_p": "p.Thr1041Ile",
"transcript": "ENST00000960871.1",
"protein_id": "ENSP00000630930.1",
"transcript_support_level": null,
"aa_start": 1041,
"aa_end": null,
"aa_length": 1072,
"cds_start": 3122,
"cds_end": null,
"cds_length": 3219,
"cdna_start": 3264,
"cdna_end": null,
"cdna_length": 4352,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960871.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3110C>T",
"hgvs_p": "p.Thr1037Ile",
"transcript": "ENST00000889111.1",
"protein_id": "ENSP00000559170.1",
"transcript_support_level": null,
"aa_start": 1037,
"aa_end": null,
"aa_length": 1068,
"cds_start": 3110,
"cds_end": null,
"cds_length": 3207,
"cdna_start": 3144,
"cdna_end": null,
"cdna_length": 3351,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889111.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.3053C>T",
"hgvs_p": "p.Thr1018Ile",
"transcript": "ENST00000929303.1",
"protein_id": "ENSP00000599362.1",
"transcript_support_level": null,
"aa_start": 1018,
"aa_end": null,
"aa_length": 1049,
"cds_start": 3053,
"cds_end": null,
"cds_length": 3150,
"cdna_start": 3203,
"cdna_end": null,
"cdna_length": 4292,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929303.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.2999C>T",
"hgvs_p": "p.Thr1000Ile",
"transcript": "ENST00000889110.1",
"protein_id": "ENSP00000559169.1",
"transcript_support_level": null,
"aa_start": 1000,
"aa_end": null,
"aa_length": 1031,
"cds_start": 2999,
"cds_end": null,
"cds_length": 3096,
"cdna_start": 3002,
"cdna_end": null,
"cdna_length": 4091,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889110.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.2873C>T",
"hgvs_p": "p.Thr958Ile",
"transcript": "ENST00000929302.1",
"protein_id": "ENSP00000599361.1",
"transcript_support_level": null,
"aa_start": 958,
"aa_end": null,
"aa_length": 989,
"cds_start": 2873,
"cds_end": null,
"cds_length": 2970,
"cdna_start": 3043,
"cdna_end": null,
"cdna_length": 4126,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929302.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.2843C>T",
"hgvs_p": "p.Thr948Ile",
"transcript": "NM_001297594.2",
"protein_id": "NP_001284523.1",
"transcript_support_level": null,
"aa_start": 948,
"aa_end": null,
"aa_length": 979,
"cds_start": 2843,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 3273,
"cdna_end": null,
"cdna_length": 4362,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001297594.2"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.2843C>T",
"hgvs_p": "p.Thr948Ile",
"transcript": "ENST00000502949.5",
"protein_id": "ENSP00000425438.1",
"transcript_support_level": 2,
"aa_start": 948,
"aa_end": null,
"aa_length": 979,
"cds_start": 2843,
"cds_end": null,
"cds_length": 2940,
"cdna_start": 3244,
"cdna_end": null,
"cdna_length": 3500,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502949.5"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.2471C>T",
"hgvs_p": "p.Thr824Ile",
"transcript": "ENST00000889112.1",
"protein_id": "ENSP00000559171.1",
"transcript_support_level": null,
"aa_start": 824,
"aa_end": null,
"aa_length": 855,
"cds_start": 2471,
"cds_end": null,
"cds_length": 2568,
"cdna_start": 2474,
"cdna_end": null,
"cdna_length": 2690,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889112.1"
},
{
"aa_ref": "T",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "c.2306C>T",
"hgvs_p": "p.Thr769Ile",
"transcript": "ENST00000960870.1",
"protein_id": "ENSP00000630929.1",
"transcript_support_level": null,
"aa_start": 769,
"aa_end": null,
"aa_length": 800,
"cds_start": 2306,
"cds_end": null,
"cds_length": 2403,
"cdna_start": 2471,
"cdna_end": null,
"cdna_length": 3557,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960870.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "n.281C>T",
"hgvs_p": null,
"transcript": "ENST00000512286.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 739,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000512286.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "n.1256C>T",
"hgvs_p": null,
"transcript": "ENST00000513416.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000513416.5"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "n.3230+9012C>T",
"hgvs_p": null,
"transcript": "XR_001741182.3",
"protein_id": null,
"transcript_support_level": null,
"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": 6719,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001741182.3"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "n.3230+9012C>T",
"hgvs_p": null,
"transcript": "XR_007096387.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4290,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007096387.1"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "n.3411+9012C>T",
"hgvs_p": null,
"transcript": "XR_007096388.1",
"protein_id": null,
"transcript_support_level": null,
"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": 4471,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007096388.1"
},
{
"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": 25,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"hgvs_c": "n.3411+9012C>T",
"hgvs_p": null,
"transcript": "XR_007096389.1",
"protein_id": null,
"transcript_support_level": null,
"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": 6900,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007096389.1"
}
],
"gene_symbol": "SEL1L3",
"gene_hgnc_id": 29108,
"dbsnp": "rs529048834",
"frequency_reference_population": 0.00001861123,
"hom_count_reference_population": 0,
"allele_count_reference_population": 30,
"gnomad_exomes_af": 0.0000171274,
"gnomad_genomes_af": 0.0000328343,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.044062793254852295,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0786,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.547,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_015187.5",
"gene_symbol": "SEL1L3",
"hgnc_id": 29108,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3302C>T",
"hgvs_p": "p.Thr1101Ile"
}
],
"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
}