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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: 17-44350293-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=44350293&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 44350293,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000053867.8",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.415T>C",
"hgvs_p": "p.Cys139Arg",
"transcript": "NM_002087.4",
"protein_id": "NP_002078.1",
"transcript_support_level": null,
"aa_start": 139,
"aa_end": null,
"aa_length": 593,
"cds_start": 415,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": "ENST00000053867.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.415T>C",
"hgvs_p": "p.Cys139Arg",
"transcript": "ENST00000053867.8",
"protein_id": "ENSP00000053867.2",
"transcript_support_level": 1,
"aa_start": 139,
"aa_end": null,
"aa_length": 593,
"cds_start": 415,
"cds_end": null,
"cds_length": 1782,
"cdna_start": 455,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": "NM_002087.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.415T>C",
"hgvs_p": "p.Cys139Arg",
"transcript": "ENST00000589265.5",
"protein_id": "ENSP00000467616.1",
"transcript_support_level": 5,
"aa_start": 139,
"aa_end": null,
"aa_length": 436,
"cds_start": 415,
"cds_end": null,
"cds_length": 1311,
"cdna_start": 452,
"cdna_end": null,
"cdna_length": 1632,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.457T>C",
"hgvs_p": "p.Cys153Arg",
"transcript": "ENST00000587387.5",
"protein_id": "ENSP00000467431.1",
"transcript_support_level": 4,
"aa_start": 153,
"aa_end": null,
"aa_length": 190,
"cds_start": 457,
"cds_end": null,
"cds_length": 574,
"cdna_start": 497,
"cdna_end": null,
"cdna_length": 614,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.415T>C",
"hgvs_p": "p.Cys139Arg",
"transcript": "ENST00000588143.5",
"protein_id": "ENSP00000465375.1",
"transcript_support_level": 3,
"aa_start": 139,
"aa_end": null,
"aa_length": 162,
"cds_start": 415,
"cds_end": null,
"cds_length": 490,
"cdna_start": 471,
"cdna_end": null,
"cdna_length": 546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.415T>C",
"hgvs_p": "p.Cys139Arg",
"transcript": "ENST00000593167.5",
"protein_id": "ENSP00000466405.1",
"transcript_support_level": 5,
"aa_start": 139,
"aa_end": null,
"aa_length": 148,
"cds_start": 415,
"cds_end": null,
"cds_length": 447,
"cdna_start": 731,
"cdna_end": null,
"cdna_length": 763,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.415T>C",
"hgvs_p": "p.Cys139Arg",
"transcript": "ENST00000592783.5",
"protein_id": "ENSP00000467870.1",
"transcript_support_level": 4,
"aa_start": 139,
"aa_end": null,
"aa_length": 141,
"cds_start": 415,
"cds_end": null,
"cds_length": 426,
"cdna_start": 530,
"cdna_end": null,
"cdna_length": 541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "n.415T>C",
"hgvs_p": null,
"transcript": "ENST00000586782.5",
"protein_id": "ENSP00000468318.1",
"transcript_support_level": 5,
"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": 843,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "n.5T>C",
"hgvs_p": null,
"transcript": "ENST00000590984.1",
"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": 562,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.265-149T>C",
"hgvs_p": null,
"transcript": "ENST00000588237.5",
"protein_id": "ENSP00000466611.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": -4,
"cds_end": null,
"cds_length": 518,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 558,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.-248T>C",
"hgvs_p": null,
"transcript": "ENST00000586443.1",
"protein_id": "ENSP00000465673.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 387,
"cds_start": -4,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.*6T>C",
"hgvs_p": null,
"transcript": "ENST00000587518.5",
"protein_id": "ENSP00000465518.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 135,
"cds_start": -4,
"cds_end": null,
"cds_length": 409,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 526,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"hgvs_c": "c.*10T>C",
"hgvs_p": null,
"transcript": "ENST00000591740.5",
"protein_id": "ENSP00000467022.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 134,
"cds_start": -4,
"cds_end": null,
"cds_length": 405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GRN",
"gene_hgnc_id": 4601,
"dbsnp": "rs763841075",
"frequency_reference_population": 0.00014197994,
"hom_count_reference_population": 0,
"allele_count_reference_population": 229,
"gnomad_exomes_af": 0.000146404,
"gnomad_genomes_af": 0.000099209,
"gnomad_exomes_ac": 214,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.987605094909668,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.837,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9624,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.062,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BS1_Supporting",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 1,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS1_Supporting"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000053867.8",
"gene_symbol": "GRN",
"hgnc_id": 4601,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.415T>C",
"hgvs_p": "p.Cys139Arg"
}
],
"clinvar_disease": "GRN-related disorder,GRN-related frontotemporal lobar degeneration with Tdp43 inclusions,Inborn genetic diseases,Neuronal ceroid lipofuscinosis 11,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:8",
"phenotype_combined": "GRN-related frontotemporal lobar degeneration with Tdp43 inclusions;Neuronal ceroid lipofuscinosis 11|not provided|GRN-related frontotemporal lobar degeneration with Tdp43 inclusions|GRN-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}