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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: 7-42937503-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=42937503&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 42937503,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_031903.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "c.494C>T",
"hgvs_p": "p.Pro165Leu",
"transcript": "NM_031903.3",
"protein_id": "NP_114109.1",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 188,
"cds_start": 494,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000223324.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_031903.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "c.494C>T",
"hgvs_p": "p.Pro165Leu",
"transcript": "ENST00000223324.3",
"protein_id": "ENSP00000223324.2",
"transcript_support_level": 1,
"aa_start": 165,
"aa_end": null,
"aa_length": 188,
"cds_start": 494,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_031903.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000223324.3"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "c.488C>T",
"hgvs_p": "p.Pro163Leu",
"transcript": "ENST00000900012.1",
"protein_id": "ENSP00000570071.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 186,
"cds_start": 488,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000900012.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "c.488C>T",
"hgvs_p": "p.Pro163Leu",
"transcript": "ENST00000921963.1",
"protein_id": "ENSP00000592022.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 186,
"cds_start": 488,
"cds_end": null,
"cds_length": 561,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000921963.1"
},
{
"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": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "n.*248C>T",
"hgvs_p": null,
"transcript": "ENST00000413995.1",
"protein_id": "ENSP00000391562.1",
"transcript_support_level": 2,
"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": "ENST00000413995.1"
},
{
"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": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "n.*2275C>T",
"hgvs_p": null,
"transcript": "ENST00000432845.1",
"protein_id": "ENSP00000415581.1",
"transcript_support_level": 2,
"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": "ENST00000432845.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "n.583C>T",
"hgvs_p": null,
"transcript": "NR_156497.1",
"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": "NR_156497.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "n.*248C>T",
"hgvs_p": null,
"transcript": "ENST00000413995.1",
"protein_id": "ENSP00000391562.1",
"transcript_support_level": 2,
"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": "ENST00000413995.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "n.*2275C>T",
"hgvs_p": null,
"transcript": "ENST00000432845.1",
"protein_id": "ENSP00000415581.1",
"transcript_support_level": 2,
"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": "ENST00000432845.1"
},
{
"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": "MRPL32",
"gene_hgnc_id": 14035,
"hgvs_c": "n.94+2367C>T",
"hgvs_p": null,
"transcript": "ENST00000496564.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000496564.1"
}
],
"gene_symbol": "MRPL32",
"gene_hgnc_id": 14035,
"dbsnp": "rs549081927",
"frequency_reference_population": 0.00011710051,
"hom_count_reference_population": 1,
"allele_count_reference_population": 189,
"gnomad_exomes_af": 0.000120398,
"gnomad_genomes_af": 0.000085424,
"gnomad_exomes_ac": 176,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.042028456926345825,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.247,
"revel_prediction": "Benign",
"alphamissense_score": 0.089,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.13,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.251,
"phylop100way_prediction": "Uncertain_significance",
"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": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_031903.3",
"gene_symbol": "MRPL32",
"hgnc_id": 14035,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.494C>T",
"hgvs_p": "p.Pro165Leu"
}
],
"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
}