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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: 12-82895907-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=82895907&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 82895907,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_152588.3",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.744C>A",
"hgvs_p": "p.Asn248Lys",
"transcript": "NM_152588.3",
"protein_id": "NP_689801.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 836,
"cds_start": 744,
"cds_end": null,
"cds_length": 2511,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000321196.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152588.3"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.744C>A",
"hgvs_p": "p.Asn248Lys",
"transcript": "ENST00000321196.8",
"protein_id": "ENSP00000322300.3",
"transcript_support_level": 1,
"aa_start": 248,
"aa_end": null,
"aa_length": 836,
"cds_start": 744,
"cds_end": null,
"cds_length": 2511,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152588.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000321196.8"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.726C>A",
"hgvs_p": "p.Asn242Lys",
"transcript": "ENST00000549919.1",
"protein_id": "ENSP00000447609.1",
"transcript_support_level": 1,
"aa_start": 242,
"aa_end": null,
"aa_length": 830,
"cds_start": 726,
"cds_end": null,
"cds_length": 2493,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000549919.1"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.744C>A",
"hgvs_p": "p.Asn248Lys",
"transcript": "ENST00000548305.5",
"protein_id": "ENSP00000448292.1",
"transcript_support_level": 1,
"aa_start": 248,
"aa_end": null,
"aa_length": 637,
"cds_start": 744,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000548305.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "n.*65C>A",
"hgvs_p": null,
"transcript": "ENST00000546590.2",
"protein_id": "ENSP00000448630.2",
"transcript_support_level": 1,
"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": "ENST00000546590.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "n.1451C>A",
"hgvs_p": null,
"transcript": "ENST00000551915.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000551915.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "n.*65C>A",
"hgvs_p": null,
"transcript": "ENST00000546590.2",
"protein_id": "ENSP00000448630.2",
"transcript_support_level": 1,
"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": "ENST00000546590.2"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.744C>A",
"hgvs_p": "p.Asn248Lys",
"transcript": "NM_001320322.2",
"protein_id": "NP_001307251.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 637,
"cds_start": 744,
"cds_end": null,
"cds_length": 1914,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320322.2"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.9C>A",
"hgvs_p": "p.Asn3Lys",
"transcript": "NM_001320321.2",
"protein_id": "NP_001307250.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 591,
"cds_start": 9,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001320321.2"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.393C>A",
"hgvs_p": "p.Asn131Lys",
"transcript": "XM_017018884.3",
"protein_id": "XP_016874373.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 719,
"cds_start": 393,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017018884.3"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.393C>A",
"hgvs_p": "p.Asn131Lys",
"transcript": "XM_024448863.2",
"protein_id": "XP_024304631.1",
"transcript_support_level": null,
"aa_start": 131,
"aa_end": null,
"aa_length": 719,
"cds_start": 393,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024448863.2"
},
{
"aa_ref": "N",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"hgvs_c": "c.744C>A",
"hgvs_p": "p.Asn248Lys",
"transcript": "XM_047428396.1",
"protein_id": "XP_047284352.1",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 700,
"cds_start": 744,
"cds_end": null,
"cds_length": 2103,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428396.1"
}
],
"gene_symbol": "TMTC2",
"gene_hgnc_id": 25440,
"dbsnp": "rs577005102",
"frequency_reference_population": 0.000051427516,
"hom_count_reference_population": 0,
"allele_count_reference_population": 83,
"gnomad_exomes_af": 0.0000492523,
"gnomad_genomes_af": 0.0000723399,
"gnomad_exomes_ac": 72,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2407119870185852,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.152,
"revel_prediction": "Benign",
"alphamissense_score": 0.3411,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.37,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.57,
"phylop100way_prediction": "Benign",
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_152588.3",
"gene_symbol": "TMTC2",
"hgnc_id": 25440,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.744C>A",
"hgvs_p": "p.Asn248Lys"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}