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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: 17-63880477-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=63880477&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 63880477,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_022557.4",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "K",
"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": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.498T>G",
"hgvs_p": "p.Asn166Lys",
"transcript": "NM_002059.5",
"protein_id": "NP_002050.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 217,
"cds_start": 498,
"cds_end": null,
"cds_length": 654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000423893.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_002059.5"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"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": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.498T>G",
"hgvs_p": "p.Asn166Lys",
"transcript": "ENST00000423893.7",
"protein_id": "ENSP00000409294.2",
"transcript_support_level": 1,
"aa_start": 166,
"aa_end": null,
"aa_length": 217,
"cds_start": 498,
"cds_end": null,
"cds_length": 654,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_002059.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000423893.7"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.751T>G",
"hgvs_p": "p.Ser251Ala",
"transcript": "ENST00000332800.7",
"protein_id": "ENSP00000333157.7",
"transcript_support_level": 1,
"aa_start": 251,
"aa_end": null,
"aa_length": 256,
"cds_start": 751,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000332800.7"
},
{
"aa_ref": "I",
"aa_alt": "S",
"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": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.494T>G",
"hgvs_p": "p.Ile165Ser",
"transcript": "ENST00000456543.6",
"protein_id": "ENSP00000394122.2",
"transcript_support_level": 1,
"aa_start": 165,
"aa_end": null,
"aa_length": 245,
"cds_start": 494,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000456543.6"
},
{
"aa_ref": "N",
"aa_alt": "K",
"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": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.453T>G",
"hgvs_p": "p.Asn151Lys",
"transcript": "ENST00000449787.6",
"protein_id": "ENSP00000410618.2",
"transcript_support_level": 1,
"aa_start": 151,
"aa_end": null,
"aa_length": 202,
"cds_start": 453,
"cds_end": null,
"cds_length": 609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000449787.6"
},
{
"aa_ref": "S",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.751T>G",
"hgvs_p": "p.Ser251Ala",
"transcript": "NM_022557.4",
"protein_id": "NP_072051.1",
"transcript_support_level": null,
"aa_start": 251,
"aa_end": null,
"aa_length": 256,
"cds_start": 751,
"cds_end": null,
"cds_length": 771,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022557.4"
},
{
"aa_ref": "I",
"aa_alt": "S",
"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": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.494T>G",
"hgvs_p": "p.Ile165Ser",
"transcript": "NM_022558.4",
"protein_id": "NP_072052.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 245,
"cds_start": 494,
"cds_end": null,
"cds_length": 738,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022558.4"
},
{
"aa_ref": "N",
"aa_alt": "K",
"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": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.453T>G",
"hgvs_p": "p.Asn151Lys",
"transcript": "NM_022556.4",
"protein_id": "NP_072050.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 202,
"cds_start": 453,
"cds_end": null,
"cds_length": 609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022556.4"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GH2",
"gene_hgnc_id": 4262,
"hgvs_c": "c.378T>G",
"hgvs_p": "p.Asn126Lys",
"transcript": "ENST00000622506.4",
"protein_id": "ENSP00000481086.1",
"transcript_support_level": 5,
"aa_start": 126,
"aa_end": null,
"aa_length": 177,
"cds_start": 378,
"cds_end": null,
"cds_length": 534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000622506.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303037",
"gene_hgnc_id": null,
"hgvs_c": "n.-6A>C",
"hgvs_p": null,
"transcript": "ENST00000791330.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000791330.1"
}
],
"gene_symbol": "GH2",
"gene_hgnc_id": 4262,
"dbsnp": "rs569201043",
"frequency_reference_population": 0.00003284223,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000328408,
"gnomad_genomes_af": 0.0000328558,
"gnomad_exomes_ac": 48,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.03749850392341614,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.184,
"revel_prediction": "Benign",
"alphamissense_score": 0.0685,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.351,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_022557.4",
"gene_symbol": "GH2",
"hgnc_id": 4262,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.751T>G",
"hgvs_p": "p.Ser251Ala"
},
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000791330.1",
"gene_symbol": "ENSG00000303037",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-6A>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}