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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: 20-34281110-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=34281110&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 34281110,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000217426.7",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1223A>G",
"hgvs_p": "p.Lys408Arg",
"transcript": "NM_000687.4",
"protein_id": "NP_000678.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 432,
"cds_start": 1223,
"cds_end": null,
"cds_length": 1299,
"cdna_start": 1308,
"cdna_end": null,
"cdna_length": 2150,
"mane_select": "ENST00000217426.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1223A>G",
"hgvs_p": "p.Lys408Arg",
"transcript": "ENST00000217426.7",
"protein_id": "ENSP00000217426.2",
"transcript_support_level": 1,
"aa_start": 408,
"aa_end": null,
"aa_length": 432,
"cds_start": 1223,
"cds_end": null,
"cds_length": 1299,
"cdna_start": 1308,
"cdna_end": null,
"cdna_length": 2150,
"mane_select": "NM_000687.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1229A>G",
"hgvs_p": "p.Lys410Arg",
"transcript": "NM_001322086.2",
"protein_id": "NP_001309015.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 434,
"cds_start": 1229,
"cds_end": null,
"cds_length": 1305,
"cdna_start": 2439,
"cdna_end": null,
"cdna_length": 3281,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1223A>G",
"hgvs_p": "p.Lys408Arg",
"transcript": "NM_001362750.2",
"protein_id": "NP_001349679.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 432,
"cds_start": 1223,
"cds_end": null,
"cds_length": 1299,
"cdna_start": 1308,
"cdna_end": null,
"cdna_length": 1774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1139A>G",
"hgvs_p": "p.Lys380Arg",
"transcript": "NM_001161766.2",
"protein_id": "NP_001155238.1",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 404,
"cds_start": 1139,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 1526,
"cdna_end": null,
"cdna_length": 2368,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1139A>G",
"hgvs_p": "p.Lys380Arg",
"transcript": "NM_001322084.2",
"protein_id": "NP_001309013.1",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 404,
"cds_start": 1139,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 2428,
"cdna_end": null,
"cdna_length": 3270,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1139A>G",
"hgvs_p": "p.Lys380Arg",
"transcript": "NM_001322085.2",
"protein_id": "NP_001309014.1",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 404,
"cds_start": 1139,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 2250,
"cdna_end": null,
"cdna_length": 3092,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1139A>G",
"hgvs_p": "p.Lys380Arg",
"transcript": "ENST00000538132.1",
"protein_id": "ENSP00000442820.1",
"transcript_support_level": 2,
"aa_start": 380,
"aa_end": null,
"aa_length": 404,
"cds_start": 1139,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 1526,
"cdna_end": null,
"cdna_length": 2366,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1223A>G",
"hgvs_p": "p.Lys408Arg",
"transcript": "XM_017027709.3",
"protein_id": "XP_016883198.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 432,
"cds_start": 1223,
"cds_end": null,
"cds_length": 1299,
"cdna_start": 1308,
"cdna_end": null,
"cdna_length": 6672,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1223A>G",
"hgvs_p": "p.Lys408Arg",
"transcript": "XM_047439962.1",
"protein_id": "XP_047295918.1",
"transcript_support_level": null,
"aa_start": 408,
"aa_end": null,
"aa_length": 432,
"cds_start": 1223,
"cds_end": null,
"cds_length": 1299,
"cdna_start": 1308,
"cdna_end": null,
"cdna_length": 4441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "c.1139A>G",
"hgvs_p": "p.Lys380Arg",
"transcript": "XM_011528659.2",
"protein_id": "XP_011526961.1",
"transcript_support_level": null,
"aa_start": 380,
"aa_end": null,
"aa_length": 404,
"cds_start": 1139,
"cds_end": null,
"cds_length": 1215,
"cdna_start": 1214,
"cdna_end": null,
"cdna_length": 2056,
"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": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"hgvs_c": "n.1371A>G",
"hgvs_p": null,
"transcript": "ENST00000480653.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 2211,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000250917",
"gene_hgnc_id": null,
"hgvs_c": "n.64A>G",
"hgvs_p": null,
"transcript": "ENST00000512005.1",
"protein_id": null,
"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": 478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AHCY",
"gene_hgnc_id": 343,
"dbsnp": "rs373929711",
"frequency_reference_population": 0.000019206891,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000198386,
"gnomad_genomes_af": 0.0000131403,
"gnomad_exomes_ac": 29,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.41357123851776123,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.321,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0696,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.459,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000217426.7",
"gene_symbol": "AHCY",
"hgnc_id": 343,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1223A>G",
"hgvs_p": "p.Lys408Arg"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000512005.1",
"gene_symbol": "ENSG00000250917",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.64A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Hypermethioninemia with deficiency of S-adenosylhomocysteine hydrolase",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}