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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: 15-79889221-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=79889221&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MTHFS",
"hgnc_id": 7437,
"hgvs_c": "c.251G>T",
"hgvs_p": "p.Arg84Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_006441.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ST20-MTHFS",
"hgnc_id": 44655,
"hgvs_c": "c.179G>T",
"hgvs_p": "p.Arg60Leu",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_001199760.2",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.144,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"chr": "15",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.09547990560531616,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 203,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2301,
"cdna_start": 277,
"cds_end": null,
"cds_length": 612,
"cds_start": 251,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_006441.4",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "c.251G>T",
"hgvs_p": "p.Arg84Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000258874.4",
"protein_coding": true,
"protein_id": "NP_006432.1",
"strand": false,
"transcript": "NM_006441.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 203,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2301,
"cdna_start": 277,
"cds_end": null,
"cds_length": 612,
"cds_start": 251,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000258874.4",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "c.251G>T",
"hgvs_p": "p.Arg84Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006441.4",
"protein_coding": true,
"protein_id": "ENSP00000258874.4",
"strand": false,
"transcript": "ENST00000258874.4",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 179,
"aa_ref": "R",
"aa_start": 60,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 859,
"cdna_start": 483,
"cds_end": null,
"cds_length": 540,
"cds_start": 179,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000479961.1",
"gene_hgnc_id": 44655,
"gene_symbol": "ST20-MTHFS",
"hgvs_c": "c.179G>T",
"hgvs_p": "p.Arg60Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000455643.1",
"strand": false,
"transcript": "ENST00000479961.1",
"transcript_support_level": 3
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 232,
"aa_ref": "R",
"aa_start": 113,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 948,
"cdna_start": 353,
"cds_end": null,
"cds_length": 699,
"cds_start": 338,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000559722.2",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "c.338G>T",
"hgvs_p": "p.Arg113Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489076.1",
"strand": false,
"transcript": "ENST00000559722.2",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 194,
"aa_ref": "R",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 803,
"cdna_start": 256,
"cds_end": null,
"cds_length": 585,
"cds_start": 251,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000877638.1",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "c.251G>T",
"hgvs_p": "p.Arg84Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547697.1",
"strand": false,
"transcript": "ENST00000877638.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 179,
"aa_ref": "R",
"aa_start": 60,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2268,
"cdna_start": 244,
"cds_end": null,
"cds_length": 540,
"cds_start": 179,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001199760.2",
"gene_hgnc_id": 44655,
"gene_symbol": "ST20-MTHFS",
"hgvs_c": "c.179G>T",
"hgvs_p": "p.Arg60Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001186689.1",
"strand": false,
"transcript": "NM_001199760.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 179,
"aa_ref": "R",
"aa_start": 60,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 679,
"cdna_start": 258,
"cds_end": null,
"cds_length": 540,
"cds_start": 179,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000615374.5",
"gene_hgnc_id": 44655,
"gene_symbol": "ST20-MTHFS",
"hgvs_c": "c.179G>T",
"hgvs_p": "p.Arg60Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489525.1",
"strand": false,
"transcript": "ENST00000615374.5",
"transcript_support_level": 3
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 169,
"aa_ref": "R",
"aa_start": 50,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 797,
"cdna_start": 205,
"cds_end": null,
"cds_length": 510,
"cds_start": 149,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000877637.1",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "c.149G>T",
"hgvs_p": "p.Arg50Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547696.1",
"strand": false,
"transcript": "ENST00000877637.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 146,
"aa_ref": "R",
"aa_start": 27,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2283,
"cdna_start": 259,
"cds_end": null,
"cds_length": 441,
"cds_start": 80,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001199758.1",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "c.80G>T",
"hgvs_p": "p.Arg27Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001186687.1",
"strand": false,
"transcript": "NM_001199758.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 121,
"aa_ref": "R",
"aa_start": 58,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 632,
"cdna_start": 437,
"cds_end": null,
"cds_length": 368,
"cds_start": 173,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000494999.1",
"gene_hgnc_id": 44655,
"gene_symbol": "ST20-MTHFS",
"hgvs_c": "c.173G>T",
"hgvs_p": "p.Arg58Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000489298.1",
"strand": false,
"transcript": "ENST00000494999.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 470,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000560919.5",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "n.*197G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454626.1",
"strand": false,
"transcript": "ENST00000560919.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2382,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NR_037654.2",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "n.358G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_037654.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 470,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000560919.5",
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"hgvs_c": "n.*197G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454626.1",
"strand": false,
"transcript": "ENST00000560919.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs751600310",
"effect": "missense_variant",
"frequency_reference_population": 6.8404506e-7,
"gene_hgnc_id": 7437,
"gene_symbol": "MTHFS",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84045e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.176,
"pos": 79889221,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.085,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_006441.4"
}
]
}