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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: 3-112169290-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=112169290&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 112169290,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_183061.3",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2958T>A",
"hgvs_p": "p.Phe986Leu",
"transcript": "NM_183061.3",
"protein_id": "NP_898884.1",
"transcript_support_level": null,
"aa_start": 986,
"aa_end": null,
"aa_length": 1177,
"cds_start": 2958,
"cds_end": null,
"cds_length": 3534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000305815.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_183061.3"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2958T>A",
"hgvs_p": "p.Phe986Leu",
"transcript": "ENST00000305815.10",
"protein_id": "ENSP00000306627.5",
"transcript_support_level": 2,
"aa_start": 986,
"aa_end": null,
"aa_length": 1177,
"cds_start": 2958,
"cds_end": null,
"cds_length": 3534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_183061.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000305815.10"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2814T>A",
"hgvs_p": "p.Phe938Leu",
"transcript": "ENST00000487372.5",
"protein_id": "ENSP00000420688.1",
"transcript_support_level": 1,
"aa_start": 938,
"aa_end": null,
"aa_length": 1129,
"cds_start": 2814,
"cds_end": null,
"cds_length": 3390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000487372.5"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2814T>A",
"hgvs_p": "p.Phe938Leu",
"transcript": "NM_001320531.2",
"protein_id": "NP_001307460.1",
"transcript_support_level": null,
"aa_start": 938,
"aa_end": null,
"aa_length": 1129,
"cds_start": 2814,
"cds_end": null,
"cds_length": 3390,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320531.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2829T>A",
"hgvs_p": "p.Phe943Leu",
"transcript": "XM_017006246.2",
"protein_id": "XP_016861735.1",
"transcript_support_level": null,
"aa_start": 943,
"aa_end": null,
"aa_length": 1134,
"cds_start": 2829,
"cds_end": null,
"cds_length": 3405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006246.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2796T>A",
"hgvs_p": "p.Phe932Leu",
"transcript": "XM_011512718.2",
"protein_id": "XP_011511020.1",
"transcript_support_level": null,
"aa_start": 932,
"aa_end": null,
"aa_length": 1123,
"cds_start": 2796,
"cds_end": null,
"cds_length": 3372,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512718.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2787T>A",
"hgvs_p": "p.Phe929Leu",
"transcript": "XM_011512719.2",
"protein_id": "XP_011511021.1",
"transcript_support_level": null,
"aa_start": 929,
"aa_end": null,
"aa_length": 1120,
"cds_start": 2787,
"cds_end": null,
"cds_length": 3363,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512719.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2772T>A",
"hgvs_p": "p.Phe924Leu",
"transcript": "XM_017006247.2",
"protein_id": "XP_016861736.1",
"transcript_support_level": null,
"aa_start": 924,
"aa_end": null,
"aa_length": 1115,
"cds_start": 2772,
"cds_end": null,
"cds_length": 3348,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006247.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2562T>A",
"hgvs_p": "p.Phe854Leu",
"transcript": "XM_017006248.2",
"protein_id": "XP_016861737.1",
"transcript_support_level": null,
"aa_start": 854,
"aa_end": null,
"aa_length": 1045,
"cds_start": 2562,
"cds_end": null,
"cds_length": 3138,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006248.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.1551T>A",
"hgvs_p": "p.Phe517Leu",
"transcript": "XM_011512725.2",
"protein_id": "XP_011511027.1",
"transcript_support_level": null,
"aa_start": 517,
"aa_end": null,
"aa_length": 708,
"cds_start": 1551,
"cds_end": null,
"cds_length": 2127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512725.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.*1287T>A",
"hgvs_p": null,
"transcript": "ENST00000471295.1",
"protein_id": "ENSP00000418371.1",
"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": "ENST00000471295.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.2228T>A",
"hgvs_p": null,
"transcript": "NR_135297.2",
"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_135297.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.*1287T>A",
"hgvs_p": null,
"transcript": "ENST00000471295.1",
"protein_id": "ENSP00000418371.1",
"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": "ENST00000471295.1"
}
],
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"dbsnp": "rs144423530",
"frequency_reference_population": 0.007591123,
"hom_count_reference_population": 70,
"allele_count_reference_population": 12246,
"gnomad_exomes_af": 0.0077415,
"gnomad_genomes_af": 0.00614942,
"gnomad_exomes_ac": 11309,
"gnomad_genomes_ac": 937,
"gnomad_exomes_homalt": 59,
"gnomad_genomes_homalt": 11,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.015887707471847534,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10999999940395355,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.432,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7419,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.949,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.11,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_183061.3",
"gene_symbol": "SLC9C1",
"hgnc_id": 31401,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2958T>A",
"hgvs_p": "p.Phe986Leu"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}