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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: 15-79889094-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=79889094&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 79889094,
"ref": "T",
"alt": "C",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_006441.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.378A>G",
"hgvs_p": "p.Thr126Thr",
"transcript": "NM_006441.4",
"protein_id": "NP_006432.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 203,
"cds_start": 378,
"cds_end": null,
"cds_length": 612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000258874.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006441.4"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.378A>G",
"hgvs_p": "p.Thr126Thr",
"transcript": "ENST00000258874.4",
"protein_id": "ENSP00000258874.4",
"transcript_support_level": 1,
"aa_start": 126,
"aa_end": null,
"aa_length": 203,
"cds_start": 378,
"cds_end": null,
"cds_length": 612,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006441.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000258874.4"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"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.306A>G",
"hgvs_p": "p.Thr102Thr",
"transcript": "ENST00000479961.1",
"protein_id": "ENSP00000455643.1",
"transcript_support_level": 3,
"aa_start": 102,
"aa_end": null,
"aa_length": 179,
"cds_start": 306,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000479961.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.465A>G",
"hgvs_p": "p.Thr155Thr",
"transcript": "ENST00000559722.2",
"protein_id": "ENSP00000489076.1",
"transcript_support_level": 2,
"aa_start": 155,
"aa_end": null,
"aa_length": 232,
"cds_start": 465,
"cds_end": null,
"cds_length": 699,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000559722.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.378A>G",
"hgvs_p": "p.Thr126Thr",
"transcript": "ENST00000877638.1",
"protein_id": "ENSP00000547697.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 194,
"cds_start": 378,
"cds_end": null,
"cds_length": 585,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877638.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"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.306A>G",
"hgvs_p": "p.Thr102Thr",
"transcript": "NM_001199760.2",
"protein_id": "NP_001186689.1",
"transcript_support_level": null,
"aa_start": 102,
"aa_end": null,
"aa_length": 179,
"cds_start": 306,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199760.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"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.306A>G",
"hgvs_p": "p.Thr102Thr",
"transcript": "ENST00000615374.5",
"protein_id": "ENSP00000489525.1",
"transcript_support_level": 3,
"aa_start": 102,
"aa_end": null,
"aa_length": 179,
"cds_start": 306,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000615374.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.276A>G",
"hgvs_p": "p.Thr92Thr",
"transcript": "ENST00000877637.1",
"protein_id": "ENSP00000547696.1",
"transcript_support_level": null,
"aa_start": 92,
"aa_end": null,
"aa_length": 169,
"cds_start": 276,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877637.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "c.207A>G",
"hgvs_p": "p.Thr69Thr",
"transcript": "NM_001199758.1",
"protein_id": "NP_001186687.1",
"transcript_support_level": null,
"aa_start": 69,
"aa_end": null,
"aa_length": 146,
"cds_start": 207,
"cds_end": null,
"cds_length": 441,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199758.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"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.300A>G",
"hgvs_p": "p.Thr100Thr",
"transcript": "ENST00000494999.1",
"protein_id": "ENSP00000489298.1",
"transcript_support_level": 3,
"aa_start": 100,
"aa_end": null,
"aa_length": 121,
"cds_start": 300,
"cds_end": null,
"cds_length": 368,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494999.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "n.*324A>G",
"hgvs_p": null,
"transcript": "ENST00000560919.5",
"protein_id": "ENSP00000454626.1",
"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": "ENST00000560919.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "n.485A>G",
"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": 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_037654.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"hgvs_c": "n.*324A>G",
"hgvs_p": null,
"transcript": "ENST00000560919.5",
"protein_id": "ENSP00000454626.1",
"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": "ENST00000560919.5"
}
],
"gene_symbol": "MTHFS",
"gene_hgnc_id": 7437,
"dbsnp": "rs138155613",
"frequency_reference_population": 0.00006876684,
"hom_count_reference_population": 0,
"allele_count_reference_population": 111,
"gnomad_exomes_af": 0.0000410447,
"gnomad_genomes_af": 0.000334804,
"gnomad_exomes_ac": 60,
"gnomad_genomes_ac": 51,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7300000190734863,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.31200000643730164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.12,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0440289110148751,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_006441.4",
"gene_symbol": "MTHFS",
"hgnc_id": 7437,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.378A>G",
"hgvs_p": "p.Thr126Thr"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_001199760.2",
"gene_symbol": "ST20-MTHFS",
"hgnc_id": 44655,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.306A>G",
"hgvs_p": "p.Thr102Thr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}