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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: 2-61826479-CTCT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=61826479&ref=CTCT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 61826479,
"ref": "CTCT",
"alt": "C",
"effect": "disruptive_inframe_deletion",
"transcript": "ENST00000404929.6",
"consequences": [
{
"aa_ref": "EE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "c.2124_2126delAGA",
"hgvs_p": "p.Glu709del",
"transcript": "NM_001201543.2",
"protein_id": "NP_001188472.1",
"transcript_support_level": null,
"aa_start": 708,
"aa_end": null,
"aa_length": 716,
"cds_start": 2124,
"cds_end": null,
"cds_length": 2151,
"cdna_start": 2145,
"cdna_end": null,
"cdna_length": 3777,
"mane_select": "ENST00000404929.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EE",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "c.2124_2126delAGA",
"hgvs_p": "p.Glu709del",
"transcript": "ENST00000404929.6",
"protein_id": "ENSP00000385158.1",
"transcript_support_level": 1,
"aa_start": 708,
"aa_end": null,
"aa_length": 716,
"cds_start": 2124,
"cds_end": null,
"cds_length": 2151,
"cdna_start": 2145,
"cdna_end": null,
"cdna_length": 3777,
"mane_select": "NM_001201543.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "c.1956_1958delAGA",
"hgvs_p": "p.Glu653del",
"transcript": "ENST00000405894.3",
"protein_id": "ENSP00000385893.3",
"transcript_support_level": 1,
"aa_start": 652,
"aa_end": null,
"aa_length": 660,
"cds_start": 1956,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 2060,
"cdna_end": null,
"cdna_length": 3684,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "n.*1471_*1473delAGA",
"hgvs_p": null,
"transcript": "ENST00000456262.5",
"protein_id": "ENSP00000396105.1",
"transcript_support_level": 1,
"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": 3579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "n.*1471_*1473delAGA",
"hgvs_p": null,
"transcript": "ENST00000456262.5",
"protein_id": "ENSP00000396105.1",
"transcript_support_level": 1,
"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": 3579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "EE",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "c.1956_1958delAGA",
"hgvs_p": "p.Glu653del",
"transcript": "NM_032180.3",
"protein_id": "NP_115556.2",
"transcript_support_level": null,
"aa_start": 652,
"aa_end": null,
"aa_length": 660,
"cds_start": 1956,
"cds_end": null,
"cds_length": 1983,
"cdna_start": 1977,
"cdna_end": null,
"cdna_length": 3609,
"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": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "n.*596_*598delAGA",
"hgvs_p": null,
"transcript": "ENST00000418113.5",
"protein_id": "ENSP00000416861.1",
"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": 4027,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "n.1919_1921delAGA",
"hgvs_p": null,
"transcript": "NR_037710.2",
"protein_id": null,
"transcript_support_level": null,
"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": 3553,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "n.*596_*598delAGA",
"hgvs_p": null,
"transcript": "ENST00000418113.5",
"protein_id": "ENSP00000416861.1",
"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": 4027,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "c.1838+622_1838+624delAGA",
"hgvs_p": null,
"transcript": "XM_047445962.1",
"protein_id": "XP_047301918.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 690,
"cds_start": -4,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "n.2025+622_2025+624delAGA",
"hgvs_p": null,
"transcript": "XR_001738972.3",
"protein_id": null,
"transcript_support_level": null,
"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": 2882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"hgvs_c": "n.2025+622_2025+624delAGA",
"hgvs_p": null,
"transcript": "XR_007082540.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FAM161A",
"gene_hgnc_id": 25808,
"dbsnp": "rs558080743",
"frequency_reference_population": 0.00092090294,
"hom_count_reference_population": 4,
"allele_count_reference_population": 1483,
"gnomad_exomes_af": 0.000934138,
"gnomad_genomes_af": 0.000794234,
"gnomad_exomes_ac": 1362,
"gnomad_genomes_ac": 121,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 2,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 0.712,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": "Likely_benign",
"acmg_criteria": "PM4_Supporting,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PM4_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000404929.6",
"gene_symbol": "FAM161A",
"hgnc_id": 25808,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2124_2126delAGA",
"hgvs_p": "p.Glu709del"
}
],
"clinvar_disease": "Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 28,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Retinitis pigmentosa 28|Retinitis pigmentosa|not provided|Retinal dystrophy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}