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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: 16-58516482-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=58516482&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 58516482,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001160305.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "NM_001160305.4",
"protein_id": "NP_001153777.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 473,
"cds_start": 481,
"cds_end": null,
"cds_length": 1422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000219315.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001160305.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "ENST00000219315.9",
"protein_id": "ENSP00000219315.5",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 473,
"cds_start": 481,
"cds_end": null,
"cds_length": 1422,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001160305.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000219315.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "n.409G>A",
"hgvs_p": null,
"transcript": "ENST00000427443.5",
"protein_id": "ENSP00000398033.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000427443.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.409G>A",
"hgvs_p": "p.Glu137Lys",
"transcript": "NM_024860.3",
"protein_id": "NP_079136.2",
"transcript_support_level": null,
"aa_start": 137,
"aa_end": null,
"aa_length": 449,
"cds_start": 409,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024860.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.409G>A",
"hgvs_p": "p.Glu137Lys",
"transcript": "ENST00000310682.6",
"protein_id": "ENSP00000310082.2",
"transcript_support_level": 2,
"aa_start": 137,
"aa_end": null,
"aa_length": 449,
"cds_start": 409,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000310682.6"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "ENST00000898783.1",
"protein_id": "ENSP00000568842.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 365,
"cds_start": 481,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898783.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "XM_047434663.1",
"protein_id": "XP_047290619.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 286,
"cds_start": 481,
"cds_end": null,
"cds_length": 861,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434663.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "XM_047434664.1",
"protein_id": "XP_047290620.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 273,
"cds_start": 481,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434664.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "XM_011523336.2",
"protein_id": "XP_011521638.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 272,
"cds_start": 481,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011523336.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "XM_047434665.1",
"protein_id": "XP_047290621.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 272,
"cds_start": 481,
"cds_end": null,
"cds_length": 819,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434665.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys",
"transcript": "XM_047434666.1",
"protein_id": "XP_047290622.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 267,
"cds_start": 481,
"cds_end": null,
"cds_length": 804,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434666.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.*34G>A",
"hgvs_p": null,
"transcript": "XM_047434667.1",
"protein_id": "XP_047290623.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 244,
"cds_start": null,
"cds_end": null,
"cds_length": 735,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047434667.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.476+139G>A",
"hgvs_p": null,
"transcript": "ENST00000898782.1",
"protein_id": "ENSP00000568841.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 408,
"cds_start": null,
"cds_end": null,
"cds_length": 1227,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898782.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.405-131G>A",
"hgvs_p": null,
"transcript": "ENST00000394266.8",
"protein_id": "ENSP00000377809.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 404,
"cds_start": null,
"cds_end": null,
"cds_length": 1215,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000394266.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.476+139G>A",
"hgvs_p": null,
"transcript": "ENST00000898781.1",
"protein_id": "ENSP00000568840.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 378,
"cds_start": null,
"cds_end": null,
"cds_length": 1137,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898781.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.169+139G>A",
"hgvs_p": null,
"transcript": "ENST00000938454.1",
"protein_id": "ENSP00000608513.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 205,
"cds_start": null,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000938454.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "c.259+139G>A",
"hgvs_p": null,
"transcript": "ENST00000447443.1",
"protein_id": "ENSP00000396437.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 182,
"cds_start": null,
"cds_end": null,
"cds_length": 551,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000447443.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "n.400G>A",
"hgvs_p": null,
"transcript": "ENST00000418480.1",
"protein_id": null,
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000418480.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "n.454G>A",
"hgvs_p": null,
"transcript": "ENST00000422445.5",
"protein_id": "ENSP00000412858.1",
"transcript_support_level": 5,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000422445.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "n.351G>A",
"hgvs_p": null,
"transcript": "ENST00000467320.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000467320.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "n.581G>A",
"hgvs_p": null,
"transcript": "ENST00000470003.5",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000470003.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"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": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "n.661G>A",
"hgvs_p": null,
"transcript": "ENST00000492050.5",
"protein_id": null,
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000492050.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"hgvs_c": "n.468G>A",
"hgvs_p": null,
"transcript": "NR_134583.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_134583.1"
}
],
"gene_symbol": "SETD6",
"gene_hgnc_id": 26116,
"dbsnp": "rs147467868",
"frequency_reference_population": 0.000570011,
"hom_count_reference_population": 6,
"allele_count_reference_population": 920,
"gnomad_exomes_af": 0.000586981,
"gnomad_genomes_af": 0.000407123,
"gnomad_exomes_ac": 858,
"gnomad_genomes_ac": 62,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011703789234161377,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.071,
"revel_prediction": "Benign",
"alphamissense_score": 0.0788,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.995,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001160305.4",
"gene_symbol": "SETD6",
"hgnc_id": 26116,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown",
"hgvs_c": "c.481G>A",
"hgvs_p": "p.Glu161Lys"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}