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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: 19-38343681-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=38343681&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CATSPERG",
"hgnc_id": 25243,
"hgvs_c": "c.426G>A",
"hgvs_p": "p.Glu142Glu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_021185.5",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_score": -3,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "19",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8199999928474426,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 1159,
"aa_ref": "E",
"aa_start": 142,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3691,
"cdna_start": 486,
"cds_end": null,
"cds_length": 3480,
"cds_start": 426,
"consequences": [
"synonymous_variant"
],
"exon_count": 29,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_021185.5",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "c.426G>A",
"hgvs_p": "p.Glu142Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000409235.8",
"protein_coding": true,
"protein_id": "NP_067008.3",
"strand": true,
"transcript": "NM_021185.5",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 1159,
"aa_ref": "E",
"aa_start": 142,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3691,
"cdna_start": 486,
"cds_end": null,
"cds_length": 3480,
"cds_start": 426,
"consequences": [
"synonymous_variant"
],
"exon_count": 29,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000409235.8",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "c.426G>A",
"hgvs_p": "p.Glu142Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_021185.5",
"protein_coding": true,
"protein_id": "ENSP00000386962.3",
"strand": true,
"transcript": "ENST00000409235.8",
"transcript_support_level": 5
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 659,
"aa_ref": "E",
"aa_start": 142,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2634,
"cdna_start": 1078,
"cds_end": null,
"cds_length": 1982,
"cds_start": 426,
"consequences": [
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000409410.6",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "c.426G>A",
"hgvs_p": "p.Glu142Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000386950.2",
"strand": true,
"transcript": "ENST00000409410.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2899,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 26,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000412458.6",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.15G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000395093.2",
"strand": true,
"transcript": "ENST00000412458.6",
"transcript_support_level": 1
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 1119,
"aa_ref": "E",
"aa_start": 142,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3571,
"cdna_start": 486,
"cds_end": null,
"cds_length": 3360,
"cds_start": 426,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001330496.2",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "c.426G>A",
"hgvs_p": "p.Glu142Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317425.1",
"strand": true,
"transcript": "NM_001330496.2",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 1119,
"aa_ref": "E",
"aa_start": 142,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3626,
"cdna_start": 541,
"cds_end": null,
"cds_length": 3360,
"cds_start": 426,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000410018.5",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "c.426G>A",
"hgvs_p": "p.Glu142Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000387057.1",
"strand": true,
"transcript": "ENST00000410018.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3501,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 29,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000312265.9",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.357G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000311314.5",
"strand": true,
"transcript": "ENST00000312265.9",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 633,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000466060.5",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.54G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000466060.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3785,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 28,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000471517.5",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.*68G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468028.1",
"strand": true,
"transcript": "ENST00000471517.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 668,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000475343.6",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.357G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000467947.1",
"strand": true,
"transcript": "ENST00000475343.6",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3785,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 28,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000471517.5",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.*68G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000468028.1",
"strand": true,
"transcript": "ENST00000471517.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 722,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000488473.1",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.-146G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000488473.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 452,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000475646.1",
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"hgvs_c": "n.-68G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000475646.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1191706385",
"effect": "synonymous_variant",
"frequency_reference_population": 7.147636e-7,
"gene_hgnc_id": 25243,
"gene_symbol": "CATSPERG",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 7.14764e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.2,
"pos": 38343681,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_021185.5"
}
]
}