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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: 11-125904566-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=125904566&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 125904566,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_013264.5",
"consequences": [
{
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp",
"transcript": "NM_013264.5",
"protein_id": "NP_037396.3",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 483,
"cds_start": 49,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263576.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_013264.5"
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp",
"transcript": "ENST00000263576.11",
"protein_id": "ENSP00000263576.6",
"transcript_support_level": 1,
"aa_start": 17,
"aa_end": null,
"aa_length": 483,
"cds_start": 49,
"cds_end": null,
"cds_length": 1452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_013264.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263576.11"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.58C>T",
"hgvs_p": "p.Arg20Trp",
"transcript": "ENST00000530414.5",
"protein_id": "ENSP00000463333.1",
"transcript_support_level": 2,
"aa_start": 20,
"aa_end": null,
"aa_length": 468,
"cds_start": 58,
"cds_end": null,
"cds_length": 1407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000530414.5"
},
{
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp",
"transcript": "ENST00000942563.1",
"protein_id": "ENSP00000612622.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 441,
"cds_start": 49,
"cds_end": null,
"cds_length": 1326,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942563.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp",
"transcript": "ENST00000910614.1",
"protein_id": "ENSP00000580673.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 420,
"cds_start": 49,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910614.1"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp",
"transcript": "ENST00000927046.1",
"protein_id": "ENSP00000597105.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 290,
"cds_start": 49,
"cds_end": null,
"cds_length": 873,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927046.1"
},
{
"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": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp",
"transcript": "XM_047426849.1",
"protein_id": "XP_047282805.1",
"transcript_support_level": null,
"aa_start": 17,
"aa_end": null,
"aa_length": 465,
"cds_start": 49,
"cds_end": null,
"cds_length": 1398,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426849.1"
},
{
"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": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.-279-646C>T",
"hgvs_p": null,
"transcript": "NM_001330438.2",
"protein_id": "NP_001317367.1",
"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": "NM_001330438.2"
},
{
"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": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.-279-646C>T",
"hgvs_p": null,
"transcript": "ENST00000525943.1",
"protein_id": "ENSP00000490224.1",
"transcript_support_level": 5,
"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": "ENST00000525943.1"
},
{
"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": "DDX25-AS1",
"gene_hgnc_id": 58188,
"hgvs_c": "n.395-1197G>A",
"hgvs_p": null,
"transcript": "ENST00000533033.2",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000533033.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "n.-212-987C>T",
"hgvs_p": null,
"transcript": "ENST00000637851.1",
"protein_id": "ENSP00000490392.1",
"transcript_support_level": 5,
"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": "nonsense_mediated_decay",
"feature": "ENST00000637851.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"hgvs_c": "c.-103C>T",
"hgvs_p": null,
"transcript": "ENST00000530129.6",
"protein_id": "ENSP00000432800.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 190,
"cds_start": null,
"cds_end": null,
"cds_length": 574,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000530129.6"
}
],
"gene_symbol": "DDX25",
"gene_hgnc_id": 18698,
"dbsnp": "rs762319891",
"frequency_reference_population": 0.000026287773,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": 0.0000262878,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.09165427088737488,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.07000000029802322,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.13,
"revel_prediction": "Benign",
"alphamissense_score": 0.1175,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.031,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_013264.5",
"gene_symbol": "DDX25",
"hgnc_id": 18698,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.49C>T",
"hgvs_p": "p.Arg17Trp"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000533033.2",
"gene_symbol": "DDX25-AS1",
"hgnc_id": 58188,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.395-1197G>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
}