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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: 19-43639781-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=43639781&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 43639781,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_145296.2",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "NM_145296.2",
"protein_id": "NP_660339.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 388,
"cds_start": 10,
"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000222374.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_145296.2"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "ENST00000222374.3",
"protein_id": "ENSP00000222374.1",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 388,
"cds_start": 10,
"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_145296.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000222374.3"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "ENST00000904152.1",
"protein_id": "ENSP00000574211.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 403,
"cds_start": 10,
"cds_end": null,
"cds_length": 1212,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904152.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "ENST00000904153.1",
"protein_id": "ENSP00000574212.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 395,
"cds_start": 10,
"cds_end": null,
"cds_length": 1188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904153.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "ENST00000904156.1",
"protein_id": "ENSP00000574215.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 381,
"cds_start": 10,
"cds_end": null,
"cds_length": 1146,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904156.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "ENST00000904155.1",
"protein_id": "ENSP00000574214.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 345,
"cds_start": 10,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904155.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "ENST00000904157.1",
"protein_id": "ENSP00000574216.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 343,
"cds_start": 10,
"cds_end": null,
"cds_length": 1032,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904157.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "ENST00000904154.1",
"protein_id": "ENSP00000574213.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 339,
"cds_start": 10,
"cds_end": null,
"cds_length": 1020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904154.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "XM_005258620.3",
"protein_id": "XP_005258677.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 345,
"cds_start": 10,
"cds_end": null,
"cds_length": 1038,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005258620.3"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser",
"transcript": "XM_047438387.1",
"protein_id": "XP_047294343.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 336,
"cds_start": 10,
"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": "XM_047438387.1"
},
{
"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": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"hgvs_c": "c.7+2182G>T",
"hgvs_p": null,
"transcript": "XM_017026452.1",
"protein_id": "XP_016881941.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 369,
"cds_start": null,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017026452.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000308028",
"gene_hgnc_id": null,
"hgvs_c": "n.-146C>A",
"hgvs_p": null,
"transcript": "ENST00000830541.1",
"protein_id": null,
"transcript_support_level": null,
"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": "pseudogene",
"feature": "ENST00000830541.1"
}
],
"gene_symbol": "CADM4",
"gene_hgnc_id": 30825,
"dbsnp": "rs771204818",
"frequency_reference_population": 0.0000011475312,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0.00000114753,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06699788570404053,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.023,
"revel_prediction": "Benign",
"alphamissense_score": 0.0928,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.081,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_145296.2",
"gene_symbol": "CADM4",
"hgnc_id": 30825,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.10G>T",
"hgvs_p": "p.Ala4Ser"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000830541.1",
"gene_symbol": "ENSG00000308028",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-146C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}