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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: 7-1898251-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=1898251&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 1898251,
"ref": "G",
"alt": "C",
"effect": "stop_gained",
"transcript": "ENST00000265854.12",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*",
"transcript": "NM_001013836.2",
"protein_id": "NP_001013858.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 718,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2210,
"cdna_end": null,
"cdna_length": 2695,
"mane_select": "ENST00000265854.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*",
"transcript": "ENST00000265854.12",
"protein_id": "ENSP00000265854.7",
"transcript_support_level": 1,
"aa_start": 649,
"aa_end": null,
"aa_length": 718,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2210,
"cdna_end": null,
"cdna_length": 2695,
"mane_select": "NM_001013836.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*",
"transcript": "ENST00000406869.5",
"protein_id": "ENSP00000385334.1",
"transcript_support_level": 1,
"aa_start": 649,
"aa_end": null,
"aa_length": 718,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2505,
"cdna_end": null,
"cdna_length": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286192",
"gene_hgnc_id": null,
"hgvs_c": "n.*4707C>G",
"hgvs_p": null,
"transcript": "ENST00000651235.1",
"protein_id": "ENSP00000498895.1",
"transcript_support_level": null,
"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": 5697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000286192",
"gene_hgnc_id": null,
"hgvs_c": "n.*4707C>G",
"hgvs_p": null,
"transcript": "ENST00000651235.1",
"protein_id": "ENSP00000498895.1",
"transcript_support_level": null,
"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": 5697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*",
"transcript": "NM_001013837.2",
"protein_id": "NP_001013859.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 718,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2207,
"cdna_end": null,
"cdna_length": 2692,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*",
"transcript": "NM_001304523.2",
"protein_id": "NP_001291452.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 718,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2031,
"cdna_end": null,
"cdna_length": 2516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*",
"transcript": "NM_003550.3",
"protein_id": "NP_003541.2",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 718,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2247,
"cdna_end": null,
"cdna_length": 2732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*",
"transcript": "ENST00000399654.6",
"protein_id": "ENSP00000382562.2",
"transcript_support_level": 5,
"aa_start": 649,
"aa_end": null,
"aa_length": 718,
"cds_start": 1947,
"cds_end": null,
"cds_length": 2157,
"cdna_start": 2276,
"cdna_end": null,
"cdna_length": 2762,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1671C>G",
"hgvs_p": "p.Tyr557*",
"transcript": "NM_001304524.2",
"protein_id": "NP_001291453.1",
"transcript_support_level": null,
"aa_start": 557,
"aa_end": null,
"aa_length": 626,
"cds_start": 1671,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1869,
"cdna_end": null,
"cdna_length": 2354,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.1671C>G",
"hgvs_p": "p.Tyr557*",
"transcript": "ENST00000402746.5",
"protein_id": "ENSP00000384155.1",
"transcript_support_level": 2,
"aa_start": 557,
"aa_end": null,
"aa_length": 626,
"cds_start": 1671,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1869,
"cdna_end": null,
"cdna_length": 2355,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.315C>G",
"hgvs_p": "p.Tyr105*",
"transcript": "NM_001304525.2",
"protein_id": "NP_001291454.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 174,
"cds_start": 315,
"cds_end": null,
"cds_length": 525,
"cdna_start": 835,
"cdna_end": null,
"cdna_length": 1320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "c.315C>G",
"hgvs_p": "p.Tyr105*",
"transcript": "ENST00000437877.1",
"protein_id": "ENSP00000394069.1",
"transcript_support_level": 2,
"aa_start": 105,
"aa_end": null,
"aa_length": 121,
"cds_start": 315,
"cds_end": null,
"cds_length": 366,
"cdna_start": 813,
"cdna_end": null,
"cdna_length": 864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"hgvs_c": "n.652C>G",
"hgvs_p": null,
"transcript": "ENST00000450235.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 850,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MAD1L1",
"gene_hgnc_id": 6762,
"dbsnp": "rs121908981",
"frequency_reference_population": 0.00003779458,
"hom_count_reference_population": 0,
"allele_count_reference_population": 61,
"gnomad_exomes_af": 0.000038994,
"gnomad_genomes_af": 0.0000262767,
"gnomad_exomes_ac": 57,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6000000238418579,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.588,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000265854.12",
"gene_symbol": "MAD1L1",
"hgnc_id": 6762,
"effects": [
"stop_gained"
],
"inheritance_mode": "Unknown,AR",
"hgvs_c": "c.1947C>G",
"hgvs_p": "p.Tyr649*"
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000651235.1",
"gene_symbol": "ENSG00000286192",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*4707C>G",
"hgvs_p": null
}
],
"clinvar_disease": " DIFFUSE LARGE B-CELL, SOMATIC,LYMPHOMA",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "LYMPHOMA, DIFFUSE LARGE B-CELL, SOMATIC",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}