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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: 1-151172270-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=151172270&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 151172270,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000295314.9",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Ser162Asn",
"transcript": "NM_013353.3",
"protein_id": "NP_037485.2",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 345,
"cds_start": 485,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 1232,
"mane_select": "ENST00000295314.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Ser162Asn",
"transcript": "ENST00000295314.9",
"protein_id": "ENSP00000295314.4",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 345,
"cds_start": 485,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 1232,
"mane_select": "NM_013353.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "c.44G>A",
"hgvs_p": "p.Ser15Asn",
"transcript": "ENST00000466891.5",
"protein_id": "ENSP00000468006.1",
"transcript_support_level": 5,
"aa_start": 15,
"aa_end": null,
"aa_length": 122,
"cds_start": 44,
"cds_end": null,
"cds_length": 369,
"cdna_start": 46,
"cdna_end": null,
"cdna_length": 441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Ser162Asn",
"transcript": "XM_011509449.2",
"protein_id": "XP_011507751.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 345,
"cds_start": 485,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 557,
"cdna_end": null,
"cdna_length": 1204,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Ser162Asn",
"transcript": "XM_047418672.1",
"protein_id": "XP_047274628.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 345,
"cds_start": 485,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 1591,
"cdna_end": null,
"cdna_length": 2238,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Ser162Asn",
"transcript": "XM_017001090.3",
"protein_id": "XP_016856579.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 261,
"cds_start": 485,
"cds_end": null,
"cds_length": 786,
"cdna_start": 585,
"cdna_end": null,
"cdna_length": 980,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "n.*337G>A",
"hgvs_p": null,
"transcript": "ENST00000463543.5",
"protein_id": "ENSP00000468489.1",
"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": 1183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "n.372G>A",
"hgvs_p": null,
"transcript": "ENST00000488488.1",
"protein_id": null,
"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": 613,
"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": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "n.*337G>A",
"hgvs_p": null,
"transcript": "ENST00000463543.5",
"protein_id": "ENSP00000468489.1",
"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": 1183,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"hgvs_c": "c.*59G>A",
"hgvs_p": null,
"transcript": "ENST00000441701.1",
"protein_id": "ENSP00000406333.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 141,
"cds_start": -4,
"cds_end": null,
"cds_length": 426,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 493,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMOD4",
"gene_hgnc_id": 11874,
"dbsnp": "rs115496308",
"frequency_reference_population": 0.000026042118,
"hom_count_reference_population": 0,
"allele_count_reference_population": 42,
"gnomad_exomes_af": 0.0000136941,
"gnomad_genomes_af": 0.000144463,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05286890268325806,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.06199999898672104,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.095,
"revel_prediction": "Benign",
"alphamissense_score": 0.1061,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.996,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0350533659205969,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000295314.9",
"gene_symbol": "TMOD4",
"hgnc_id": 11874,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.485G>A",
"hgvs_p": "p.Ser162Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}