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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: X-119837941-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=119837941&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 119837941,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000276201.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373His",
"transcript": "NM_080632.3",
"protein_id": "NP_542199.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 483,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 2343,
"mane_select": "ENST00000276201.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373His",
"transcript": "ENST00000276201.7",
"protein_id": "ENSP00000276201.3",
"transcript_support_level": 1,
"aa_start": 373,
"aa_end": null,
"aa_length": 483,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 2343,
"mane_select": "NM_080632.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1079G>A",
"hgvs_p": "p.Arg360His",
"transcript": "ENST00000345865.6",
"protein_id": "ENSP00000245418.2",
"transcript_support_level": 1,
"aa_start": 360,
"aa_end": null,
"aa_length": 470,
"cds_start": 1079,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 2335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1079G>A",
"hgvs_p": "p.Arg360His",
"transcript": "NM_023010.4",
"protein_id": "NP_075386.1",
"transcript_support_level": null,
"aa_start": 360,
"aa_end": null,
"aa_length": 470,
"cds_start": 1079,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 1114,
"cdna_end": null,
"cdna_length": 2304,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373His",
"transcript": "XM_017029737.2",
"protein_id": "XP_016885226.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 643,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1932,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 1968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373His",
"transcript": "XM_017029738.2",
"protein_id": "XP_016885227.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 641,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 2097,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373His",
"transcript": "XM_047442375.1",
"protein_id": "XP_047298331.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 641,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 4136,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1079G>A",
"hgvs_p": "p.Arg360His",
"transcript": "XM_017029739.2",
"protein_id": "XP_016885228.1",
"transcript_support_level": null,
"aa_start": 360,
"aa_end": null,
"aa_length": 630,
"cds_start": 1079,
"cds_end": null,
"cds_length": 1893,
"cdna_start": 1114,
"cdna_end": null,
"cdna_length": 1929,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373His",
"transcript": "XM_017029740.2",
"protein_id": "XP_016885229.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 609,
"cds_start": 1118,
"cds_end": null,
"cds_length": 1830,
"cdna_start": 1153,
"cdna_end": null,
"cdna_length": 1866,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "UPF3B",
"gene_hgnc_id": 20439,
"dbsnp": "rs146785878",
"frequency_reference_population": 0.000038885075,
"hom_count_reference_population": 14,
"allele_count_reference_population": 47,
"gnomad_exomes_af": 0.0000300661,
"gnomad_genomes_af": 0.000126005,
"gnomad_exomes_ac": 33,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4043658673763275,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.393,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3788,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.222,
"phylop100way_prediction": "Uncertain_significance",
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000276201.7",
"gene_symbol": "UPF3B",
"hgnc_id": 20439,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1118G>A",
"hgvs_p": "p.Arg373His"
}
],
"clinvar_disease": "Inborn genetic diseases,Syndromic X-linked intellectual disability 14,UPF3B-related disorder",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "Syndromic X-linked intellectual disability 14|UPF3B-related disorder|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}