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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: 5-79121329-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=79121329&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "BHMT",
"hgnc_id": 1047,
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_001713.3",
"verdict": "Benign"
},
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "DMGDH",
"hgnc_id": 24475,
"hgvs_c": "n.152G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "ENST00000518707.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 2653,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0605,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.85,
"chr": "5",
"clinvar_classification": "Benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0040801167488098145,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 406,
"aa_ref": "P",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2470,
"cdna_start": 666,
"cds_end": null,
"cds_length": 1221,
"cds_start": 589,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001713.3",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000274353.10",
"protein_coding": true,
"protein_id": "NP_001704.2",
"strand": true,
"transcript": "NM_001713.3",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 406,
"aa_ref": "P",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2470,
"cdna_start": 666,
"cds_end": null,
"cds_length": 1221,
"cds_start": 589,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000274353.10",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001713.3",
"protein_coding": true,
"protein_id": "ENSP00000274353.5",
"strand": true,
"transcript": "ENST00000274353.10",
"transcript_support_level": 1
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 405,
"aa_ref": "P",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2466,
"cdna_start": 666,
"cds_end": null,
"cds_length": 1218,
"cds_start": 589,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000910530.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580589.1",
"strand": true,
"transcript": "ENST00000910530.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 404,
"aa_ref": "P",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2465,
"cdna_start": 668,
"cds_end": null,
"cds_length": 1215,
"cds_start": 589,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000910525.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580584.1",
"strand": true,
"transcript": "ENST00000910525.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 404,
"aa_ref": "P",
"aa_start": 195,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2463,
"cdna_start": 660,
"cds_end": null,
"cds_length": 1215,
"cds_start": 583,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000910528.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.583C>T",
"hgvs_p": "p.Pro195Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580587.1",
"strand": true,
"transcript": "ENST00000910528.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 368,
"aa_ref": "P",
"aa_start": 159,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2355,
"cdna_start": 552,
"cds_end": null,
"cds_length": 1107,
"cds_start": 475,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000910529.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.475C>T",
"hgvs_p": "p.Pro159Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580588.1",
"strand": true,
"transcript": "ENST00000910529.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 354,
"aa_ref": "P",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2315,
"cdna_start": 666,
"cds_end": null,
"cds_length": 1065,
"cds_start": 589,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000910526.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580585.1",
"strand": true,
"transcript": "ENST00000910526.1",
"transcript_support_level": null
},
{
"aa_alt": "S",
"aa_end": null,
"aa_length": 345,
"aa_ref": "P",
"aa_start": 197,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2286,
"cdna_start": 666,
"cds_end": null,
"cds_length": 1038,
"cds_start": 589,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000910527.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.589C>T",
"hgvs_p": "p.Pro197Ser",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000580586.1",
"strand": true,
"transcript": "ENST00000910527.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 253,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1207,
"cdna_start": null,
"cds_end": null,
"cds_length": 762,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000524080.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "c.167-4717C>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000428240.1",
"strand": true,
"transcript": "ENST00000524080.1",
"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": 455,
"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": "ENST00000518707.1",
"gene_hgnc_id": 24475,
"gene_symbol": "DMGDH",
"hgvs_c": "n.152G>A",
"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": "ENST00000518707.1",
"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": 661,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000520388.5",
"gene_hgnc_id": 24475,
"gene_symbol": "DMGDH",
"hgvs_c": "n.252G>A",
"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": "ENST00000520388.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 711,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000521279.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "n.49C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000521279.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 590,
"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": "ENST00000523508.1",
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"hgvs_c": "n.302C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000523508.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs60947960",
"effect": "missense_variant",
"frequency_reference_population": 0.0016437728,
"gene_hgnc_id": 1047,
"gene_symbol": "BHMT",
"gnomad_exomes_ac": 1386,
"gnomad_exomes_af": 0.000948198,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_ac": 1267,
"gnomad_genomes_af": 0.00832184,
"gnomad_genomes_homalt": 15,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 29,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -2.669,
"pos": 79121329,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.093,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001713.3"
}
]
}