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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: 16-21258819-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=21258819&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 21258819,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001888.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Ala303Thr",
"transcript": "NM_001376256.1",
"protein_id": "NP_001363185.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 314,
"cds_start": 907,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000572914.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001376256.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Ala303Thr",
"transcript": "ENST00000572914.2",
"protein_id": "ENSP00000461904.2",
"transcript_support_level": 2,
"aa_start": 303,
"aa_end": null,
"aa_length": 314,
"cds_start": 907,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001376256.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000572914.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Ala303Thr",
"transcript": "ENST00000219599.8",
"protein_id": "ENSP00000219599.3",
"transcript_support_level": 1,
"aa_start": 303,
"aa_end": null,
"aa_length": 314,
"cds_start": 907,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000219599.8"
},
{
"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": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "n.*520+2435G>A",
"hgvs_p": null,
"transcript": "ENST00000574448.5",
"protein_id": "ENSP00000459982.1",
"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": "ENST00000574448.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.973G>A",
"hgvs_p": "p.Ala325Thr",
"transcript": "ENST00000903146.1",
"protein_id": "ENSP00000573205.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 336,
"cds_start": 973,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903146.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Ala303Thr",
"transcript": "NM_001888.5",
"protein_id": "NP_001879.1",
"transcript_support_level": null,
"aa_start": 303,
"aa_end": null,
"aa_length": 314,
"cds_start": 907,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001888.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Ala303Thr",
"transcript": "ENST00000543948.5",
"protein_id": "ENSP00000440227.1",
"transcript_support_level": 5,
"aa_start": 303,
"aa_end": null,
"aa_length": 314,
"cds_start": 907,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000543948.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.880G>A",
"hgvs_p": "p.Ala294Thr",
"transcript": "ENST00000903145.1",
"protein_id": "ENSP00000573204.1",
"transcript_support_level": null,
"aa_start": 294,
"aa_end": null,
"aa_length": 305,
"cds_start": 880,
"cds_end": null,
"cds_length": 918,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903145.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.820G>A",
"hgvs_p": "p.Ala274Thr",
"transcript": "ENST00000903144.1",
"protein_id": "ENSP00000573203.1",
"transcript_support_level": null,
"aa_start": 274,
"aa_end": null,
"aa_length": 285,
"cds_start": 820,
"cds_end": null,
"cds_length": 858,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000903144.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.805G>A",
"hgvs_p": "p.Ala269Thr",
"transcript": "ENST00000934988.1",
"protein_id": "ENSP00000605047.1",
"transcript_support_level": null,
"aa_start": 269,
"aa_end": null,
"aa_length": 280,
"cds_start": 805,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934988.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.601G>A",
"hgvs_p": "p.Ala201Thr",
"transcript": "ENST00000934987.1",
"protein_id": "ENSP00000605046.1",
"transcript_support_level": null,
"aa_start": 201,
"aa_end": null,
"aa_length": 212,
"cds_start": 601,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000934987.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"hgvs_c": "c.232G>A",
"hgvs_p": "p.Ala78Thr",
"transcript": "ENST00000570401.5",
"protein_id": "ENSP00000460820.1",
"transcript_support_level": 5,
"aa_start": 78,
"aa_end": null,
"aa_length": 96,
"cds_start": 232,
"cds_end": null,
"cds_length": 291,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000570401.5"
}
],
"gene_symbol": "CRYM",
"gene_hgnc_id": 2418,
"dbsnp": "rs727502945",
"frequency_reference_population": 0.000032836408,
"hom_count_reference_population": 0,
"allele_count_reference_population": 53,
"gnomad_exomes_af": 0.0000342034,
"gnomad_genomes_af": 0.0000197086,
"gnomad_exomes_ac": 50,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9723491668701172,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.859,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4475,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.897,
"phylop100way_prediction": "Uncertain_significance",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BS2",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001888.5",
"gene_symbol": "CRYM",
"hgnc_id": 2418,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.907G>A",
"hgvs_p": "p.Ala303Thr"
}
],
"clinvar_disease": "Autosomal dominant nonsyndromic hearing loss 40,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:5",
"phenotype_combined": "not specified|not provided|Autosomal dominant nonsyndromic hearing loss 40",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}