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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: 19-3612141-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=3612141&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "CACTIN",
"hgnc_id": 29938,
"hgvs_c": "c.2059G>A",
"hgvs_p": "p.Asp687Asn",
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "NM_021231.2",
"verdict": "Uncertain_significance"
},
{
"benign_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "CACTIN-AS1",
"hgnc_id": 31391,
"hgvs_c": "n.605C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 0,
"transcript": "ENST00000592274.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_score": 0,
"allele_count_reference_population": 37,
"alphamissense_prediction": null,
"alphamissense_score": 0.0991,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.23287272453308105,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 758,
"aa_ref": "D",
"aa_start": 687,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3583,
"cdna_start": 2087,
"cds_end": null,
"cds_length": 2277,
"cds_start": 2059,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001080543.2",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.2059G>A",
"hgvs_p": "p.Asp687Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000429344.7",
"protein_coding": true,
"protein_id": "NP_001074012.1",
"strand": false,
"transcript": "NM_001080543.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 758,
"aa_ref": "D",
"aa_start": 687,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3583,
"cdna_start": 2087,
"cds_end": null,
"cds_length": 2277,
"cds_start": 2059,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000429344.7",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.2059G>A",
"hgvs_p": "p.Asp687Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001080543.2",
"protein_coding": true,
"protein_id": "ENSP00000415078.1",
"strand": false,
"transcript": "ENST00000429344.7",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 758,
"aa_ref": "D",
"aa_start": 687,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2797,
"cdna_start": 2112,
"cds_end": null,
"cds_length": 2277,
"cds_start": 2059,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000221899.7",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.2059G>A",
"hgvs_p": "p.Asp687Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000221899.4",
"strand": false,
"transcript": "ENST00000221899.7",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 290,
"aa_ref": "D",
"aa_start": 219,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1220,
"cdna_start": 656,
"cds_end": null,
"cds_length": 873,
"cds_start": 655,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000592721.5",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.655G>A",
"hgvs_p": "p.Asp219Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000467149.1",
"strand": false,
"transcript": "ENST00000592721.5",
"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": 2810,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 12,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000585942.5",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "n.2059G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000465751.1",
"strand": false,
"transcript": "ENST00000585942.5",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 758,
"aa_ref": "D",
"aa_start": 687,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2651,
"cdna_start": 2087,
"cds_end": null,
"cds_length": 2277,
"cds_start": 2059,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_021231.2",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.2059G>A",
"hgvs_p": "p.Asp687Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_067054.1",
"strand": false,
"transcript": "NM_021231.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 758,
"aa_ref": "D",
"aa_start": 687,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2671,
"cdna_start": 2112,
"cds_end": null,
"cds_length": 2277,
"cds_start": 2059,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000248420.9",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.2059G>A",
"hgvs_p": "p.Asp687Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000248420.5",
"strand": false,
"transcript": "ENST00000248420.9",
"transcript_support_level": 5
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 726,
"aa_ref": "D",
"aa_start": 655,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3495,
"cdna_start": 1999,
"cds_end": null,
"cds_length": 2181,
"cds_start": 1963,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000918263.1",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.1963G>A",
"hgvs_p": "p.Asp655Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000588322.1",
"strand": false,
"transcript": "ENST00000918263.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 117,
"aa_ref": "D",
"aa_start": 46,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 699,
"cdna_start": 136,
"cds_end": null,
"cds_length": 354,
"cds_start": 136,
"consequences": [
"missense_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000591726.1",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "c.136G>A",
"hgvs_p": "p.Asp46Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000464898.1",
"strand": false,
"transcript": "ENST00000591726.1",
"transcript_support_level": 5
},
{
"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": 2216,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000587175.1",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "n.1643G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000587175.1",
"transcript_support_level": 5
},
{
"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": 1708,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000589321.5",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "n.*711G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000466600.1",
"strand": false,
"transcript": "ENST00000589321.5",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1913,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000592274.1",
"gene_hgnc_id": 31391,
"gene_symbol": "CACTIN-AS1",
"hgvs_c": "n.605C>T",
"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": "ENST00000592274.1",
"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": 1913,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NR_038865.1",
"gene_hgnc_id": 31391,
"gene_symbol": "CACTIN-AS1",
"hgvs_c": "n.605C>T",
"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": "NR_038865.1",
"transcript_support_level": null
},
{
"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": 1708,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000589321.5",
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"hgvs_c": "n.*711G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000466600.1",
"strand": false,
"transcript": "ENST00000589321.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376455756",
"effect": "missense_variant",
"frequency_reference_population": 0.000022929582,
"gene_hgnc_id": 29938,
"gene_symbol": "CACTIN",
"gnomad_exomes_ac": 35,
"gnomad_exomes_af": 0.0000239502,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000131347,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.67,
"pos": 3612141,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.127,
"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_021231.2"
}
]
}