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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: 15-79845338-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=79845338&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 79845338,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000258874.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.484C>T",
"hgvs_p": "p.Gln162*",
"transcript": "NM_006441.4",
"protein_id": "NP_006432.1",
"transcript_support_level": null,
"aa_start": 162,
"aa_end": null,
"aa_length": 203,
"cds_start": 484,
"cds_end": null,
"cds_length": 612,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 2301,
"mane_select": "ENST00000258874.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.484C>T",
"hgvs_p": "p.Gln162*",
"transcript": "ENST00000258874.4",
"protein_id": "ENSP00000258874.4",
"transcript_support_level": 1,
"aa_start": 162,
"aa_end": null,
"aa_length": 203,
"cds_start": 484,
"cds_end": null,
"cds_length": 612,
"cdna_start": 510,
"cdna_end": null,
"cdna_length": 2301,
"mane_select": "NM_006441.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST20-MTHFS",
"gene_hgnc_id": 44655,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.Gln138*",
"transcript": "ENST00000479961.1",
"protein_id": "ENSP00000455643.1",
"transcript_support_level": 3,
"aa_start": 138,
"aa_end": null,
"aa_length": 179,
"cds_start": 412,
"cds_end": null,
"cds_length": 540,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 859,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.571C>T",
"hgvs_p": "p.Gln191*",
"transcript": "ENST00000559722.2",
"protein_id": "ENSP00000489076.1",
"transcript_support_level": 2,
"aa_start": 191,
"aa_end": null,
"aa_length": 232,
"cds_start": 571,
"cds_end": null,
"cds_length": 699,
"cdna_start": 586,
"cdna_end": null,
"cdna_length": 948,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST20-MTHFS",
"gene_hgnc_id": 44655,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.Gln138*",
"transcript": "NM_001199760.2",
"protein_id": "NP_001186689.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 179,
"cds_start": 412,
"cds_end": null,
"cds_length": 540,
"cdna_start": 477,
"cdna_end": null,
"cdna_length": 2268,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST20-MTHFS",
"gene_hgnc_id": 44655,
"hgvs_c": "c.412C>T",
"hgvs_p": "p.Gln138*",
"transcript": "ENST00000615374.5",
"protein_id": "ENSP00000489525.1",
"transcript_support_level": 3,
"aa_start": 138,
"aa_end": null,
"aa_length": 179,
"cds_start": 412,
"cds_end": null,
"cds_length": 540,
"cdna_start": 491,
"cdna_end": null,
"cdna_length": 679,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.313C>T",
"hgvs_p": "p.Gln105*",
"transcript": "NM_001199758.1",
"protein_id": "NP_001186687.1",
"transcript_support_level": null,
"aa_start": 105,
"aa_end": null,
"aa_length": 146,
"cds_start": 313,
"cds_end": null,
"cds_length": 441,
"cdna_start": 492,
"cdna_end": null,
"cdna_length": 2283,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "n.591C>T",
"hgvs_p": null,
"transcript": "NR_037654.2",
"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": 2382,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "n.-12C>T",
"hgvs_p": null,
"transcript": "ENST00000560261.1",
"protein_id": "ENSP00000454318.1",
"transcript_support_level": 3,
"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": 595,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ST20-MTHFS",
"gene_hgnc_id": 44655,
"hgvs_c": "c.*38C>T",
"hgvs_p": null,
"transcript": "ENST00000494999.1",
"protein_id": "ENSP00000489298.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 121,
"cds_start": -4,
"cds_end": null,
"cds_length": 368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"dbsnp": "rs771379232",
"frequency_reference_population": 0.00003283665,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000335183,
"gnomad_genomes_af": 0.0000262881,
"gnomad_exomes_ac": 49,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.46000000834465027,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.46,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.116,
"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": 8,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000258874.4",
"gene_symbol": "MTHFS",
"hgnc_id": 7437,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.484C>T",
"hgvs_p": "p.Gln162*"
},
{
"score": 8,
"benign_score": 0,
"pathogenic_score": 8,
"criteria": [
"PVS1_Strong",
"PM2",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000479961.1",
"gene_symbol": "ST20-MTHFS",
"hgnc_id": 44655,
"effects": [
"stop_gained"
],
"inheritance_mode": "",
"hgvs_c": "c.412C>T",
"hgvs_p": "p.Gln138*"
}
],
"clinvar_disease": " and hypomyelination, epilepsy,Neurodevelopmental disorder with microcephaly",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Neurodevelopmental disorder with microcephaly, epilepsy, and hypomyelination",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}