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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: 19-44623879-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=44623879&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 44623879,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001205280.2",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100Trp",
"transcript": "NM_001205280.2",
"protein_id": "NP_001192209.1",
"transcript_support_level": null,
"aa_start": 100,
"aa_end": null,
"aa_length": 192,
"cds_start": 298,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000402988.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001205280.2"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100Trp",
"transcript": "ENST00000402988.6",
"protein_id": "ENSP00000385592.1",
"transcript_support_level": 3,
"aa_start": 100,
"aa_end": null,
"aa_length": 192,
"cds_start": 298,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001205280.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402988.6"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"hgvs_c": "c.133C>T",
"hgvs_p": "p.Arg45Trp",
"transcript": "ENST00000441389.1",
"protein_id": "ENSP00000407344.1",
"transcript_support_level": 1,
"aa_start": 45,
"aa_end": null,
"aa_length": 137,
"cds_start": 133,
"cds_end": null,
"cds_length": 414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000441389.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"hgvs_c": "c.385C>T",
"hgvs_p": "p.Arg129Trp",
"transcript": "ENST00000911252.1",
"protein_id": "ENSP00000581311.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 221,
"cds_start": 385,
"cds_end": null,
"cds_length": 666,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911252.1"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"hgvs_c": "c.355C>T",
"hgvs_p": "p.Arg119Trp",
"transcript": "ENST00000428245.5",
"protein_id": "ENSP00000410629.1",
"transcript_support_level": 5,
"aa_start": 119,
"aa_end": null,
"aa_length": 211,
"cds_start": 355,
"cds_end": null,
"cds_length": 636,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000428245.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"hgvs_c": "c.125+10109C>T",
"hgvs_p": null,
"transcript": "ENST00000911253.1",
"protein_id": "ENSP00000581312.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 52,
"cds_start": null,
"cds_end": null,
"cds_length": 159,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911253.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CEACAM16-AS1",
"gene_hgnc_id": 55317,
"hgvs_c": "n.379+8452G>A",
"hgvs_p": null,
"transcript": "ENST00000810360.1",
"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": "ENST00000810360.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"hgvs_c": "c.*102C>T",
"hgvs_p": null,
"transcript": "ENST00000592507.1",
"protein_id": "ENSP00000465887.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 65,
"cds_start": null,
"cds_end": null,
"cds_length": 199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000592507.1"
}
],
"gene_symbol": "IGSF23",
"gene_hgnc_id": 40040,
"dbsnp": "rs757196933",
"frequency_reference_population": 0.00013155163,
"hom_count_reference_population": 0,
"allele_count_reference_population": 204,
"gnomad_exomes_af": 0.000141573,
"gnomad_genomes_af": 0.0000394348,
"gnomad_exomes_ac": 198,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3377634882926941,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.101,
"revel_prediction": "Benign",
"alphamissense_score": 0.3451,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.625,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NM_001205280.2",
"gene_symbol": "IGSF23",
"hgnc_id": 40040,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.298C>T",
"hgvs_p": "p.Arg100Trp"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "ENST00000810360.1",
"gene_symbol": "CEACAM16-AS1",
"hgnc_id": 55317,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.379+8452G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}