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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: 14-67748644-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=67748644&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 67748644,
"ref": "C",
"alt": "G",
"effect": "splice_region_variant,intron_variant",
"transcript": "NM_015346.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.7417-5G>C",
"hgvs_p": null,
"transcript": "NM_015346.4",
"protein_id": "NP_056161.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2539,
"cds_start": null,
"cds_end": null,
"cds_length": 7620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000347230.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015346.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.7417-5G>C",
"hgvs_p": null,
"transcript": "ENST00000347230.9",
"protein_id": "ENSP00000251119.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2539,
"cds_start": null,
"cds_end": null,
"cds_length": 7620,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015346.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000347230.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 40,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "n.8172-5G>C",
"hgvs_p": null,
"transcript": "ENST00000554523.5",
"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": "ENST00000554523.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 40,
"intron_rank": 39,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "n.*5395-5G>C",
"hgvs_p": null,
"transcript": "ENST00000554557.5",
"protein_id": "ENSP00000450431.1",
"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": "ENST00000554557.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.7462-5G>C",
"hgvs_p": null,
"transcript": "ENST00000678386.1",
"protein_id": "ENSP00000503677.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2554,
"cds_start": null,
"cds_end": null,
"cds_length": 7665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000678386.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.7435-5G>C",
"hgvs_p": null,
"transcript": "ENST00000676512.1",
"protein_id": "ENSP00000504552.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2545,
"cds_start": null,
"cds_end": null,
"cds_length": 7638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676512.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.7339-5G>C",
"hgvs_p": null,
"transcript": "ENST00000676620.1",
"protein_id": "ENSP00000504587.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2513,
"cds_start": null,
"cds_end": null,
"cds_length": 7542,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000676620.1"
},
{
"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": 42,
"intron_rank": 41,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.7416+2408G>C",
"hgvs_p": null,
"transcript": "XM_047431173.1",
"protein_id": "XP_047287129.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2497,
"cds_start": null,
"cds_end": null,
"cds_length": 7494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431173.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.5092-5G>C",
"hgvs_p": null,
"transcript": "XM_047431174.1",
"protein_id": "XP_047287130.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1764,
"cds_start": null,
"cds_end": null,
"cds_length": 5295,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431174.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "c.4999-5G>C",
"hgvs_p": null,
"transcript": "XM_047431175.1",
"protein_id": "XP_047287131.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1733,
"cds_start": null,
"cds_end": null,
"cds_length": 5202,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431175.1"
},
{
"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": 15,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"hgvs_c": "n.2679+2408G>C",
"hgvs_p": null,
"transcript": "ENST00000394455.6",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000394455.6"
}
],
"gene_symbol": "ZFYVE26",
"gene_hgnc_id": 20761,
"dbsnp": "rs201771769",
"frequency_reference_population": 0.0053327815,
"hom_count_reference_population": 59,
"allele_count_reference_population": 8606,
"gnomad_exomes_af": 0.00549458,
"gnomad_genomes_af": 0.00378072,
"gnomad_exomes_ac": 8030,
"gnomad_genomes_ac": 576,
"gnomad_exomes_homalt": 52,
"gnomad_genomes_homalt": 7,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6200000047683716,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.0560000017285347,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.492,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000816421124013722,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_015346.4",
"gene_symbol": "ZFYVE26",
"hgnc_id": 20761,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.7417-5G>C",
"hgvs_p": null
}
],
"clinvar_disease": "Hereditary spastic paraplegia,Hereditary spastic paraplegia 15,Spastic paraplegia,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2 B:3",
"phenotype_combined": "not provided|Hereditary spastic paraplegia 15|Hereditary spastic paraplegia|not specified|Spastic paraplegia",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}