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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: 3-124841442-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=124841442&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 124841442,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000296181.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.721C>T",
"hgvs_p": "p.Arg241Trp",
"transcript": "NM_002213.5",
"protein_id": "NP_002204.2",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 799,
"cds_start": 721,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 4440,
"mane_select": "ENST00000296181.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.721C>T",
"hgvs_p": "p.Arg241Trp",
"transcript": "ENST00000296181.9",
"protein_id": "ENSP00000296181.4",
"transcript_support_level": 1,
"aa_start": 241,
"aa_end": null,
"aa_length": 799,
"cds_start": 721,
"cds_end": null,
"cds_length": 2400,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 4440,
"mane_select": "NM_002213.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "NM_001354764.2",
"protein_id": "NP_001341693.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 691,
"cds_start": 397,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 4158,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "NM_001354765.1",
"protein_id": "NP_001341694.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 691,
"cds_start": 397,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 736,
"cdna_end": null,
"cdna_length": 4090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "NM_001354766.2",
"protein_id": "NP_001341695.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 646,
"cds_start": 397,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 4023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.253C>T",
"hgvs_p": "p.Arg85Trp",
"transcript": "ENST00000488466.5",
"protein_id": "ENSP00000477446.1",
"transcript_support_level": 5,
"aa_start": 85,
"aa_end": null,
"aa_length": 322,
"cds_start": 253,
"cds_end": null,
"cds_length": 971,
"cdna_start": 253,
"cdna_end": null,
"cdna_length": 971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.109C>T",
"hgvs_p": "p.Arg37Trp",
"transcript": "ENST00000496703.1",
"protein_id": "ENSP00000418367.1",
"transcript_support_level": 2,
"aa_start": 37,
"aa_end": null,
"aa_length": 261,
"cds_start": 109,
"cds_end": null,
"cds_length": 788,
"cdna_start": 110,
"cdna_end": null,
"cdna_length": 789,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "ENST00000608657.5",
"protein_id": "ENSP00000477230.1",
"transcript_support_level": 3,
"aa_start": 133,
"aa_end": null,
"aa_length": 138,
"cds_start": 397,
"cds_end": null,
"cds_length": 418,
"cdna_start": 804,
"cdna_end": null,
"cdna_length": 825,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.721C>T",
"hgvs_p": "p.Arg241Trp",
"transcript": "XM_005247436.4",
"protein_id": "XP_005247493.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 769,
"cds_start": 721,
"cds_end": null,
"cds_length": 2310,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 4350,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.721C>T",
"hgvs_p": "p.Arg241Trp",
"transcript": "XM_006713630.4",
"protein_id": "XP_006713693.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 754,
"cds_start": 721,
"cds_end": null,
"cds_length": 2265,
"cdna_start": 1086,
"cdna_end": null,
"cdna_length": 4305,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "XM_017006353.2",
"protein_id": "XP_016861842.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 691,
"cds_start": 397,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 738,
"cdna_end": null,
"cdna_length": 4092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "XM_047448087.1",
"protein_id": "XP_047304043.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 691,
"cds_start": 397,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 4023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "XM_047448088.1",
"protein_id": "XP_047304044.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 661,
"cds_start": 397,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 3933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "c.397C>T",
"hgvs_p": "p.Arg133Trp",
"transcript": "XM_047448089.1",
"protein_id": "XP_047304045.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 646,
"cds_start": 397,
"cds_end": null,
"cds_length": 1941,
"cdna_start": 669,
"cdna_end": null,
"cdna_length": 3888,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "n.*356C>T",
"hgvs_p": null,
"transcript": "ENST00000465464.5",
"protein_id": "ENSP00000418079.2",
"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": 1164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"hgvs_c": "n.*356C>T",
"hgvs_p": null,
"transcript": "ENST00000465464.5",
"protein_id": "ENSP00000418079.2",
"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": 1164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ITGB5",
"gene_hgnc_id": 6160,
"dbsnp": "rs201926531",
"frequency_reference_population": 0.000120182034,
"hom_count_reference_population": 0,
"allele_count_reference_population": 194,
"gnomad_exomes_af": 0.00011971,
"gnomad_genomes_af": 0.000124716,
"gnomad_exomes_ac": 175,
"gnomad_genomes_ac": 19,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3146195411682129,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.821,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8955,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.43,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.851,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,BP4",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 1,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000296181.9",
"gene_symbol": "ITGB5",
"hgnc_id": 6160,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.721C>T",
"hgvs_p": "p.Arg241Trp"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}