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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: 19-38729348-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38729348&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 38729348,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000252699.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2652G>A",
"hgvs_p": "p.Ala884Ala",
"transcript": "NM_004924.6",
"protein_id": "NP_004915.2",
"transcript_support_level": null,
"aa_start": 884,
"aa_end": null,
"aa_length": 911,
"cds_start": 2652,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2749,
"cdna_end": null,
"cdna_length": 4990,
"mane_select": "ENST00000252699.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2652G>A",
"hgvs_p": "p.Ala884Ala",
"transcript": "ENST00000252699.7",
"protein_id": "ENSP00000252699.2",
"transcript_support_level": 1,
"aa_start": 884,
"aa_end": null,
"aa_length": 911,
"cds_start": 2652,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2749,
"cdna_end": null,
"cdna_length": 4990,
"mane_select": "NM_004924.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2652G>A",
"hgvs_p": "p.Ala884Ala",
"transcript": "ENST00000424234.7",
"protein_id": "ENSP00000411187.4",
"transcript_support_level": 1,
"aa_start": 884,
"aa_end": null,
"aa_length": 911,
"cds_start": 2652,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2738,
"cdna_end": null,
"cdna_length": 2923,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.1995G>A",
"hgvs_p": "p.Ala665Ala",
"transcript": "ENST00000390009.7",
"protein_id": "ENSP00000439497.1",
"transcript_support_level": 1,
"aa_start": 665,
"aa_end": null,
"aa_length": 692,
"cds_start": 1995,
"cds_end": null,
"cds_length": 2079,
"cdna_start": 2003,
"cdna_end": null,
"cdna_length": 2102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2718G>A",
"hgvs_p": "p.Ala906Ala",
"transcript": "NM_001440296.1",
"protein_id": "NP_001427225.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 933,
"cds_start": 2718,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2815,
"cdna_end": null,
"cdna_length": 3998,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2718G>A",
"hgvs_p": "p.Ala906Ala",
"transcript": "NM_001440300.1",
"protein_id": "NP_001427229.1",
"transcript_support_level": null,
"aa_start": 906,
"aa_end": null,
"aa_length": 933,
"cds_start": 2718,
"cds_end": null,
"cds_length": 2802,
"cdna_start": 2815,
"cdna_end": null,
"cdna_length": 3998,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2652G>A",
"hgvs_p": "p.Ala884Ala",
"transcript": "NM_001411143.1",
"protein_id": "NP_001398072.1",
"transcript_support_level": null,
"aa_start": 884,
"aa_end": null,
"aa_length": 911,
"cds_start": 2652,
"cds_end": null,
"cds_length": 2736,
"cdna_start": 2749,
"cdna_end": null,
"cdna_length": 4990,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2637G>A",
"hgvs_p": "p.Ala879Ala",
"transcript": "NM_001322033.2",
"protein_id": "NP_001308962.1",
"transcript_support_level": null,
"aa_start": 879,
"aa_end": null,
"aa_length": 906,
"cds_start": 2637,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 2734,
"cdna_end": null,
"cdna_length": 4975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2637G>A",
"hgvs_p": "p.Ala879Ala",
"transcript": "NM_001440298.1",
"protein_id": "NP_001427227.1",
"transcript_support_level": null,
"aa_start": 879,
"aa_end": null,
"aa_length": 906,
"cds_start": 2637,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 2734,
"cdna_end": null,
"cdna_length": 3917,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2637G>A",
"hgvs_p": "p.Ala879Ala",
"transcript": "ENST00000440400.3",
"protein_id": "ENSP00000398393.2",
"transcript_support_level": 5,
"aa_start": 879,
"aa_end": null,
"aa_length": 906,
"cds_start": 2637,
"cds_end": null,
"cds_length": 2721,
"cdna_start": 2734,
"cdna_end": null,
"cdna_length": 4975,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2511G>A",
"hgvs_p": "p.Ala837Ala",
"transcript": "ENST00000697712.1",
"protein_id": "ENSP00000513410.1",
"transcript_support_level": null,
"aa_start": 837,
"aa_end": null,
"aa_length": 864,
"cds_start": 2511,
"cds_end": null,
"cds_length": 2595,
"cdna_start": 2511,
"cdna_end": null,
"cdna_length": 4752,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.2400G>A",
"hgvs_p": "p.Ala800Ala",
"transcript": "NM_001440299.1",
"protein_id": "NP_001427228.1",
"transcript_support_level": null,
"aa_start": 800,
"aa_end": null,
"aa_length": 827,
"cds_start": 2400,
"cds_end": null,
"cds_length": 2484,
"cdna_start": 2792,
"cdna_end": null,
"cdna_length": 3975,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "n.471G>A",
"hgvs_p": null,
"transcript": "ENST00000477174.1",
"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": 544,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "n.405G>A",
"hgvs_p": null,
"transcript": "ENST00000497637.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"hgvs_c": "c.284-641G>A",
"hgvs_p": null,
"transcript": "ENST00000589528.1",
"protein_id": "ENSP00000467190.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 104,
"cds_start": -4,
"cds_end": null,
"cds_length": 315,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ACTN4",
"gene_hgnc_id": 166,
"dbsnp": "rs202127035",
"frequency_reference_population": 0.00009984137,
"hom_count_reference_population": 0,
"allele_count_reference_population": 161,
"gnomad_exomes_af": 0.0000917417,
"gnomad_genomes_af": 0.000177706,
"gnomad_exomes_ac": 134,
"gnomad_genomes_ac": 27,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.151,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000252699.7",
"gene_symbol": "ACTN4",
"hgnc_id": 166,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2652G>A",
"hgvs_p": "p.Ala884Ala"
}
],
"clinvar_disease": "Focal segmental glomerulosclerosis 1,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:3",
"phenotype_combined": "not provided|Focal segmental glomerulosclerosis 1",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}