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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: 3-112167249-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=112167249&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 112167249,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_183061.3",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3336T>A",
"hgvs_p": "p.His1112Gln",
"transcript": "NM_183061.3",
"protein_id": "NP_898884.1",
"transcript_support_level": null,
"aa_start": 1112,
"aa_end": null,
"aa_length": 1177,
"cds_start": 3336,
"cds_end": null,
"cds_length": 3534,
"cdna_start": 3547,
"cdna_end": null,
"cdna_length": 4119,
"mane_select": "ENST00000305815.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_183061.3"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3336T>A",
"hgvs_p": "p.His1112Gln",
"transcript": "ENST00000305815.10",
"protein_id": "ENSP00000306627.5",
"transcript_support_level": 2,
"aa_start": 1112,
"aa_end": null,
"aa_length": 1177,
"cds_start": 3336,
"cds_end": null,
"cds_length": 3534,
"cdna_start": 3547,
"cdna_end": null,
"cdna_length": 4119,
"mane_select": "NM_183061.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000305815.10"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3192T>A",
"hgvs_p": "p.His1064Gln",
"transcript": "ENST00000487372.5",
"protein_id": "ENSP00000420688.1",
"transcript_support_level": 1,
"aa_start": 1064,
"aa_end": null,
"aa_length": 1129,
"cds_start": 3192,
"cds_end": null,
"cds_length": 3390,
"cdna_start": 3414,
"cdna_end": null,
"cdna_length": 3979,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000487372.5"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3192T>A",
"hgvs_p": "p.His1064Gln",
"transcript": "NM_001320531.2",
"protein_id": "NP_001307460.1",
"transcript_support_level": null,
"aa_start": 1064,
"aa_end": null,
"aa_length": 1129,
"cds_start": 3192,
"cds_end": null,
"cds_length": 3390,
"cdna_start": 3403,
"cdna_end": null,
"cdna_length": 3975,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320531.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3207T>A",
"hgvs_p": "p.His1069Gln",
"transcript": "XM_017006246.2",
"protein_id": "XP_016861735.1",
"transcript_support_level": null,
"aa_start": 1069,
"aa_end": null,
"aa_length": 1134,
"cds_start": 3207,
"cds_end": null,
"cds_length": 3405,
"cdna_start": 3294,
"cdna_end": null,
"cdna_length": 3866,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006246.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3174T>A",
"hgvs_p": "p.His1058Gln",
"transcript": "XM_011512718.2",
"protein_id": "XP_011511020.1",
"transcript_support_level": null,
"aa_start": 1058,
"aa_end": null,
"aa_length": 1123,
"cds_start": 3174,
"cds_end": null,
"cds_length": 3372,
"cdna_start": 3385,
"cdna_end": null,
"cdna_length": 3957,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512718.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3165T>A",
"hgvs_p": "p.His1055Gln",
"transcript": "XM_011512719.2",
"protein_id": "XP_011511021.1",
"transcript_support_level": null,
"aa_start": 1055,
"aa_end": null,
"aa_length": 1120,
"cds_start": 3165,
"cds_end": null,
"cds_length": 3363,
"cdna_start": 3376,
"cdna_end": null,
"cdna_length": 3948,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011512719.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.3150T>A",
"hgvs_p": "p.His1050Gln",
"transcript": "XM_017006247.2",
"protein_id": "XP_016861736.1",
"transcript_support_level": null,
"aa_start": 1050,
"aa_end": null,
"aa_length": 1115,
"cds_start": 3150,
"cds_end": null,
"cds_length": 3348,
"cdna_start": 3361,
"cdna_end": null,
"cdna_length": 3933,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006247.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.2940T>A",
"hgvs_p": "p.His980Gln",
"transcript": "XM_017006248.2",
"protein_id": "XP_016861737.1",
"transcript_support_level": null,
"aa_start": 980,
"aa_end": null,
"aa_length": 1045,
"cds_start": 2940,
"cds_end": null,
"cds_length": 3138,
"cdna_start": 3151,
"cdna_end": null,
"cdna_length": 3723,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017006248.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "c.1929T>A",
"hgvs_p": "p.His643Gln",
"transcript": "XM_011512725.2",
"protein_id": "XP_011511027.1",
"transcript_support_level": null,
"aa_start": 643,
"aa_end": null,
"aa_length": 708,
"cds_start": 1929,
"cds_end": null,
"cds_length": 2127,
"cdna_start": 2138,
"cdna_end": null,
"cdna_length": 2710,
"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": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.*1665T>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": 2733,
"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": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.2606T>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": 3178,
"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": 19,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"hgvs_c": "n.*1665T>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": 2733,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000471295.1"
}
],
"gene_symbol": "SLC9C1",
"gene_hgnc_id": 31401,
"dbsnp": "rs932432681",
"frequency_reference_population": 0.0000012426327,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.86215e-7,
"gnomad_genomes_af": 0.00000656961,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08049836754798889,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.091,
"revel_prediction": "Benign",
"alphamissense_score": 0.0815,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.589,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_183061.3",
"gene_symbol": "SLC9C1",
"hgnc_id": 31401,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3336T>A",
"hgvs_p": "p.His1112Gln"
}
],
"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
}