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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: 16-1361875-CAAGTAT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1361875&ref=CAAGTAT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 1361875,
"ref": "CAAGTAT",
"alt": "C",
"effect": "conservative_inframe_deletion",
"transcript": "ENST00000204679.9",
"consequences": [
{
"aa_ref": "KY",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "c.238_243delAAGTAT",
"hgvs_p": "p.Lys80_Tyr81del",
"transcript": "NM_032520.5",
"protein_id": "NP_115909.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 305,
"cds_start": 238,
"cds_end": null,
"cds_length": 918,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 1975,
"mane_select": "ENST00000204679.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "KY",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "c.238_243delAAGTAT",
"hgvs_p": "p.Lys80_Tyr81del",
"transcript": "ENST00000204679.9",
"protein_id": "ENSP00000204679.4",
"transcript_support_level": 1,
"aa_start": 80,
"aa_end": null,
"aa_length": 305,
"cds_start": 238,
"cds_end": null,
"cds_length": 918,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 1975,
"mane_select": "NM_032520.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "KY",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "c.322_327delAAGTAT",
"hgvs_p": "p.Lys108_Tyr109del",
"transcript": "ENST00000529110.2",
"protein_id": "ENSP00000435349.2",
"transcript_support_level": 2,
"aa_start": 108,
"aa_end": null,
"aa_length": 333,
"cds_start": 322,
"cds_end": null,
"cds_length": 1002,
"cdna_start": 322,
"cdna_end": null,
"cdna_length": 1002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "KY",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"conservative_inframe_deletion"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "c.286_291delAAGTAT",
"hgvs_p": "p.Lys96_Tyr97del",
"transcript": "ENST00000683887.1",
"protein_id": "ENSP00000506886.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 321,
"cds_start": 286,
"cds_end": null,
"cds_length": 966,
"cdna_start": 297,
"cdna_end": null,
"cdna_length": 1237,
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.*140_*145delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000526820.5",
"protein_id": "ENSP00000434413.1",
"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": 572,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.1254_1259delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000527076.1",
"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": 2400,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.337_342delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000527168.6",
"protein_id": null,
"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": 2313,
"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": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.296_301delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000529957.6",
"protein_id": null,
"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": 1991,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.183_188delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000683366.1",
"protein_id": "ENSP00000507283.1",
"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": 2185,
"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": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.232_237delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000684100.1",
"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": 2208,
"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": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.296_301delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000684126.1",
"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": 2146,
"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": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.863_868delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000684688.1",
"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": 3926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"hgvs_c": "n.*140_*145delAAGTAT",
"hgvs_p": null,
"transcript": "ENST00000526820.5",
"protein_id": "ENSP00000434413.1",
"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": 572,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNPTG",
"gene_hgnc_id": 23026,
"dbsnp": "rs773452586",
"frequency_reference_population": 0.000066302804,
"hom_count_reference_population": 0,
"allele_count_reference_population": 107,
"gnomad_exomes_af": 0.0000649972,
"gnomad_genomes_af": 0.0000788405,
"gnomad_exomes_ac": 95,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 8.762,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"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_pathogenic",
"acmg_criteria": "PM2,PM4,PP3,PP5",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PM4",
"PP3",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000204679.9",
"gene_symbol": "GNPTG",
"hgnc_id": 23026,
"effects": [
"conservative_inframe_deletion"
],
"inheritance_mode": "AR",
"hgvs_c": "c.238_243delAAGTAT",
"hgvs_p": "p.Lys80_Tyr81del"
}
],
"clinvar_disease": "GNPTG-mucolipidosis,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:2 US:1",
"phenotype_combined": "GNPTG-mucolipidosis|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}