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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: 15-43604408-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=43604408&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 43604408,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_153700.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "c.4171C>G",
"hgvs_p": "p.Arg1391Gly",
"transcript": "NM_153700.2",
"protein_id": "NP_714544.1",
"transcript_support_level": null,
"aa_start": 1391,
"aa_end": null,
"aa_length": 1775,
"cds_start": 4171,
"cds_end": null,
"cds_length": 5328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000450892.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_153700.2"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "c.4171C>G",
"hgvs_p": "p.Arg1391Gly",
"transcript": "ENST00000450892.7",
"protein_id": "ENSP00000401513.2",
"transcript_support_level": 5,
"aa_start": 1391,
"aa_end": null,
"aa_length": 1775,
"cds_start": 4171,
"cds_end": null,
"cds_length": 5328,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_153700.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000450892.7"
},
{
"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": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "n.*1963C>G",
"hgvs_p": null,
"transcript": "ENST00000440125.5",
"protein_id": "ENSP00000394866.1",
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000440125.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "n.*1963C>G",
"hgvs_p": null,
"transcript": "ENST00000440125.5",
"protein_id": "ENSP00000394866.1",
"transcript_support_level": 1,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000440125.5"
},
{
"aa_ref": "R",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "c.1852C>G",
"hgvs_p": "p.Arg618Gly",
"transcript": "ENST00000541030.5",
"protein_id": "ENSP00000440413.1",
"transcript_support_level": 5,
"aa_start": 618,
"aa_end": null,
"aa_length": 1002,
"cds_start": 1852,
"cds_end": null,
"cds_length": 3009,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000541030.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "n.*1374C>G",
"hgvs_p": null,
"transcript": "ENST00000428650.5",
"protein_id": "ENSP00000415991.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000428650.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "n.2125C>G",
"hgvs_p": null,
"transcript": "ENST00000471703.5",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000471703.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "n.3026C>G",
"hgvs_p": null,
"transcript": "ENST00000485556.5",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000485556.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "n.*1374C>G",
"hgvs_p": null,
"transcript": "ENST00000428650.5",
"protein_id": "ENSP00000415991.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000428650.5"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CKMT1B",
"gene_hgnc_id": 1995,
"hgvs_c": "n.143-376G>C",
"hgvs_p": null,
"transcript": "ENST00000411560.1",
"protein_id": null,
"transcript_support_level": 3,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000411560.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"hgvs_c": "n.1666-2857C>G",
"hgvs_p": null,
"transcript": "ENST00000448437.6",
"protein_id": null,
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000448437.6"
}
],
"gene_symbol": "STRC",
"gene_hgnc_id": 16035,
"dbsnp": "rs376104748",
"frequency_reference_population": 0.00007561208,
"hom_count_reference_population": 2,
"allele_count_reference_population": 120,
"gnomad_exomes_af": 0.0000724562,
"gnomad_genomes_af": 0.000105473,
"gnomad_exomes_ac": 104,
"gnomad_genomes_ac": 16,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.226165771484375,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1899999976158142,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.642,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5364,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.945,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.19,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM5,PP5,BP4,BS2_Supporting",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 2,
"pathogenic_score": 3,
"criteria": [
"PM5",
"PP5",
"BP4",
"BS2_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "NM_153700.2",
"gene_symbol": "STRC",
"hgnc_id": 16035,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4171C>G",
"hgvs_p": "p.Arg1391Gly"
},
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000411560.1",
"gene_symbol": "CKMT1B",
"hgnc_id": 1995,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.143-376G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal dominant nonsyndromic hearing loss 16,Autosomal recessive nonsyndromic hearing loss 16,Deafness-infertility syndrome,Nonsyndromic genetic hearing loss,Rare genetic deafness,Spermatogenic failure 7,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:4 US:2",
"phenotype_combined": "Rare genetic deafness|Autosomal dominant nonsyndromic hearing loss 16|not provided|Autosomal recessive nonsyndromic hearing loss 16|Nonsyndromic genetic hearing loss|Autosomal recessive nonsyndromic hearing loss 16;Deafness-infertility syndrome;Spermatogenic failure 7",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}