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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: 7-23246921-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=23246921&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 23246921,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_002510.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "NM_002510.3",
"protein_id": "NP_002501.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 560,
"cds_start": 64,
"cds_end": null,
"cds_length": 1683,
"cdna_start": 147,
"cdna_end": null,
"cdna_length": 2650,
"mane_select": "ENST00000258733.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "ENST00000258733.9",
"protein_id": "ENSP00000258733.5",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 560,
"cds_start": 64,
"cds_end": null,
"cds_length": 1683,
"cdna_start": 147,
"cdna_end": null,
"cdna_length": 2650,
"mane_select": "NM_002510.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "ENST00000381990.6",
"protein_id": "ENSP00000371420.2",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 572,
"cds_start": 64,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 225,
"cdna_end": null,
"cdna_length": 2763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "ENST00000409458.3",
"protein_id": "ENSP00000386476.3",
"transcript_support_level": 1,
"aa_start": 22,
"aa_end": null,
"aa_length": 206,
"cds_start": 64,
"cds_end": null,
"cds_length": 621,
"cdna_start": 213,
"cdna_end": null,
"cdna_length": 1673,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "ENST00000647578.1",
"protein_id": "ENSP00000497362.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 588,
"cds_start": 64,
"cds_end": null,
"cds_length": 1767,
"cdna_start": 176,
"cdna_end": null,
"cdna_length": 2751,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "NM_001005340.2",
"protein_id": "NP_001005340.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 572,
"cds_start": 64,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 147,
"cdna_end": null,
"cdna_length": 2686,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "XM_047419776.1",
"protein_id": "XP_047275732.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 572,
"cds_start": 64,
"cds_end": null,
"cds_length": 1719,
"cdna_start": 110,
"cdna_end": null,
"cdna_length": 2649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "XM_005249578.4",
"protein_id": "XP_005249635.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 531,
"cds_start": 64,
"cds_end": null,
"cds_length": 1596,
"cdna_start": 147,
"cdna_end": null,
"cdna_length": 2697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser",
"transcript": "XM_017011678.3",
"protein_id": "XP_016867167.1",
"transcript_support_level": null,
"aa_start": 22,
"aa_end": null,
"aa_length": 519,
"cds_start": 64,
"cds_end": null,
"cds_length": 1560,
"cdna_start": 147,
"cdna_end": null,
"cdna_length": 2661,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "n.156G>T",
"hgvs_p": null,
"transcript": "ENST00000459927.5",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "n.148G>T",
"hgvs_p": null,
"transcript": "ENST00000474157.1",
"protein_id": null,
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "n.154G>T",
"hgvs_p": null,
"transcript": "ENST00000487890.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "n.249-6386G>T",
"hgvs_p": null,
"transcript": "ENST00000465673.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 793,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"hgvs_c": "n.273-6386G>T",
"hgvs_p": null,
"transcript": "ENST00000492858.6",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 721,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GPNMB",
"gene_hgnc_id": 4462,
"dbsnp": "rs370332714",
"frequency_reference_population": 0.000012426744,
"hom_count_reference_population": 0,
"allele_count_reference_population": 20,
"gnomad_exomes_af": 0.00000480322,
"gnomad_genomes_af": 0.0000854836,
"gnomad_exomes_ac": 7,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.16377854347229004,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.087,
"revel_prediction": "Benign",
"alphamissense_score": 0.1009,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.706,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_002510.3",
"gene_symbol": "GPNMB",
"hgnc_id": 4462,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.64G>T",
"hgvs_p": "p.Ala22Ser"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}