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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: 2-196433459-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=196433459&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PVS1_Moderate",
"BS1"
],
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"gene_symbol": "HECW2",
"hgnc_id": 29853,
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"inheritance_mode": "AR,AD",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_020760.4",
"verdict": "Likely_benign"
},
{
"benign_score": 0,
"criteria": [
"PP3_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC105373822",
"hgnc_id": null,
"hgvs_c": "n.44-2325C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 4,
"score": 4,
"transcript": "XR_923746.4",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PVS1_Moderate,BS1",
"acmg_score": -2,
"allele_count_reference_population": 14,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.33,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " and absent language, seizures,Neurodevelopmental disorder with hypotonia",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.33000001311302185,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1572,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12006,
"cdna_start": null,
"cds_end": null,
"cds_length": 4719,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001348768.2",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000644978.2",
"protein_coding": true,
"protein_id": "NP_001335697.1",
"strand": false,
"transcript": "NM_001348768.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1572,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 12006,
"cdna_start": null,
"cds_end": null,
"cds_length": 4719,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000644978.2",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001348768.2",
"protein_coding": true,
"protein_id": "ENSP00000495418.1",
"strand": false,
"transcript": "ENST00000644978.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1572,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12180,
"cdna_start": null,
"cds_end": null,
"cds_length": 4719,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000260983.8",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000260983.2",
"strand": false,
"transcript": "ENST00000260983.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1579,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6830,
"cdna_start": null,
"cds_end": null,
"cds_length": 4740,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000644030.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000495504.1",
"strand": false,
"transcript": "ENST00000644030.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1579,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11749,
"cdna_start": null,
"cds_end": null,
"cds_length": 4740,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000867916.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000537975.1",
"strand": false,
"transcript": "ENST00000867916.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1572,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12479,
"cdna_start": null,
"cds_end": null,
"cds_length": 4719,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_020760.4",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_065811.1",
"strand": false,
"transcript": "NM_020760.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1572,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6916,
"cdna_start": null,
"cds_end": null,
"cds_length": 4719,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000644256.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000494649.1",
"strand": false,
"transcript": "ENST00000644256.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1572,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7212,
"cdna_start": null,
"cds_end": null,
"cds_length": 4719,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000931760.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601819.1",
"strand": false,
"transcript": "ENST00000931760.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1527,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5165,
"cdna_start": null,
"cds_end": null,
"cds_length": 4584,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000956008.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626067.1",
"strand": false,
"transcript": "ENST00000956008.1",
"transcript_support_level": null
},
{
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"aa_length": 1488,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6744,
"cdna_start": null,
"cds_end": null,
"cds_length": 4467,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 27,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000956007.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000626066.1",
"strand": false,
"transcript": "ENST00000956007.1",
"transcript_support_level": null
},
{
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"aa_length": 119,
"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 574,
"cdna_start": null,
"cds_end": null,
"cds_length": 360,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
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"feature": "ENST00000427457.2",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000395770.2",
"strand": false,
"transcript": "ENST00000427457.2",
"transcript_support_level": 4
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12027,
"cdna_start": null,
"cds_end": null,
"cds_length": 4740,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
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"feature": "XM_006712646.4",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_006712709.1",
"strand": false,
"transcript": "XM_006712646.4",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12192,
"cdna_start": null,
"cds_end": null,
"cds_length": 4740,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024453020.2",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
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"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024308788.1",
"strand": false,
"transcript": "XM_024453020.2",
"transcript_support_level": null
},
{
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"cdna_start": null,
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"consequences": [
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"intron_variant"
],
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"feature": "XM_024453021.2",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
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"intron_rank": 1,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_024308789.1",
"strand": false,
"transcript": "XM_024453021.2",
"transcript_support_level": null
},
{
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"aa_ref": null,
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12600,
"cdna_start": null,
"cds_end": null,
"cds_length": 4740,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047445194.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301150.1",
"strand": false,
"transcript": "XM_047445194.1",
"transcript_support_level": null
},
{
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"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 29735,
"cdna_start": null,
"cds_end": null,
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"cds_start": null,
"consequences": [
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"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
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"feature": "XM_047445195.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_047301151.1",
"strand": false,
"transcript": "XM_047445195.1",
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},
{
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"consequences": [
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],
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"feature": "XM_047445196.1",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_047301152.1",
"strand": false,
"transcript": "XM_047445196.1",
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},
{
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"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
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"feature": "XM_047445197.1",
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"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
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"mane_plus": null,
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"protein_coding": true,
"protein_id": "XP_047301153.1",
"strand": false,
"transcript": "XM_047445197.1",
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},
{
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"biotype": "protein_coding",
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"cds_end": null,
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"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047445198.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "c.-35-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047301154.1",
"strand": false,
"transcript": "XM_047445198.1",
"transcript_support_level": null
},
{
"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": 4139,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 10,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000645770.1",
"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
"hgvs_c": "n.178-1G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000645770.1",
"transcript_support_level": null
},
{
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"biotype": "pseudogene",
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"consequences": [
"intron_variant"
],
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"feature": "XR_923746.4",
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"gene_symbol": "LOC105373822",
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"strand": true,
"transcript": "XR_923746.4",
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}
],
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"dbscsnv_ada_prediction": "Pathogenic",
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"dbsnp": "rs755596278",
"effect": "splice_acceptor_variant,intron_variant",
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"gene_hgnc_id": 29853,
"gene_symbol": "HECW2",
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"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Neurodevelopmental disorder with hypotonia, seizures, and absent language",
"phylop100way_prediction": "Uncertain_significance",
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"pos": 196433459,
"ref": "C",
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"splice_prediction_selected": "Pathogenic",
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"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
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"transcript": "NM_020760.4"
}
]
}