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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: 4-67753986-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=67753986&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 67753986,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000226413.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNRHR",
"gene_hgnc_id": 4421,
"hgvs_c": "c.350T>G",
"hgvs_p": "p.Leu117Arg",
"transcript": "NM_000406.3",
"protein_id": "NP_000397.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 328,
"cds_start": 350,
"cds_end": null,
"cds_length": 987,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 4402,
"mane_select": "ENST00000226413.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNRHR",
"gene_hgnc_id": 4421,
"hgvs_c": "c.350T>G",
"hgvs_p": "p.Leu117Arg",
"transcript": "ENST00000226413.5",
"protein_id": "ENSP00000226413.5",
"transcript_support_level": 1,
"aa_start": 117,
"aa_end": null,
"aa_length": 328,
"cds_start": 350,
"cds_end": null,
"cds_length": 987,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 4402,
"mane_select": "NM_000406.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNRHR",
"gene_hgnc_id": 4421,
"hgvs_c": "c.350T>G",
"hgvs_p": "p.Leu117Arg",
"transcript": "ENST00000420975.2",
"protein_id": "ENSP00000397561.2",
"transcript_support_level": 1,
"aa_start": 117,
"aa_end": null,
"aa_length": 249,
"cds_start": 350,
"cds_end": null,
"cds_length": 750,
"cdna_start": 350,
"cdna_end": null,
"cdna_length": 859,
"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": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.1921-1203A>C",
"hgvs_p": null,
"transcript": "ENST00000500538.7",
"protein_id": null,
"transcript_support_level": 1,
"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": 3434,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNRHR",
"gene_hgnc_id": 4421,
"hgvs_c": "c.350T>G",
"hgvs_p": "p.Leu117Arg",
"transcript": "NM_001012763.2",
"protein_id": "NP_001012781.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 249,
"cds_start": 350,
"cds_end": null,
"cds_length": 750,
"cdna_start": 403,
"cdna_end": null,
"cdna_length": 4017,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.335-173A>C",
"hgvs_p": null,
"transcript": "ENST00000502758.1",
"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": 547,
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.1209-173A>C",
"hgvs_p": null,
"transcript": "ENST00000660972.1",
"protein_id": null,
"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": 3477,
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.1208+21641A>C",
"hgvs_p": null,
"transcript": "ENST00000663060.2",
"protein_id": null,
"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": 2275,
"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": 10,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.1266+21641A>C",
"hgvs_p": null,
"transcript": "ENST00000667140.2",
"protein_id": null,
"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": 2670,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.488+23816A>C",
"hgvs_p": null,
"transcript": "ENST00000793751.1",
"protein_id": null,
"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": 822,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.457+23816A>C",
"hgvs_p": null,
"transcript": "ENST00000793752.1",
"protein_id": null,
"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": 858,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.398+23816A>C",
"hgvs_p": null,
"transcript": "ENST00000793753.1",
"protein_id": null,
"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": 773,
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "UBA6-DT",
"gene_hgnc_id": 49083,
"hgvs_c": "n.119-36462A>C",
"hgvs_p": null,
"transcript": "ENST00000793754.1",
"protein_id": null,
"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": 475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNRHR",
"gene_hgnc_id": 4421,
"dbsnp": "rs727505367",
"frequency_reference_population": 0.000008054962,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000752539,
"gnomad_genomes_af": 0.0000131411,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9607712626457214,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.642,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8512,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.18,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.24,
"phylop100way_prediction": "Pathogenic",
"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": 15,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 15,
"benign_score": 0,
"pathogenic_score": 15,
"criteria": [
"PM1",
"PP2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000226413.5",
"gene_symbol": "GNRHR",
"hgnc_id": 4421,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.350T>G",
"hgvs_p": "p.Leu117Arg"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000500538.7",
"gene_symbol": "UBA6-DT",
"hgnc_id": 49083,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1921-1203A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Delayed puberty,Hypogonadotropic hypogonadism 7 with or without anosmia",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Delayed puberty|Hypogonadotropic hypogonadism 7 with or without anosmia",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}