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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: 4-55364206-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=55364206&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 55364206,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_024592.5",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "NM_024592.5",
"protein_id": "NP_078868.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 318,
"cds_start": 497,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264228.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024592.5"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "ENST00000264228.9",
"protein_id": "ENSP00000264228.4",
"transcript_support_level": 1,
"aa_start": 166,
"aa_end": null,
"aa_length": 318,
"cds_start": 497,
"cds_end": null,
"cds_length": 957,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024592.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264228.9"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"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": "ENSG00000288695",
"gene_hgnc_id": null,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "ENST00000679707.1",
"protein_id": "ENSP00000505713.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 284,
"cds_start": 497,
"cds_end": null,
"cds_length": 855,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679707.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3-AS1",
"gene_hgnc_id": 44138,
"hgvs_c": "n.1382C>T",
"hgvs_p": null,
"transcript": "ENST00000433175.6",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000433175.6"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "ENST00000918496.1",
"protein_id": "ENSP00000588555.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 317,
"cds_start": 497,
"cds_end": null,
"cds_length": 954,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000918496.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "ENST00000870318.1",
"protein_id": "ENSP00000540377.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 314,
"cds_start": 497,
"cds_end": null,
"cds_length": 945,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870318.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "NM_001410732.1",
"protein_id": "NP_001397661.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 273,
"cds_start": 497,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001410732.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "ENST00000679836.1",
"protein_id": "ENSP00000506601.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 273,
"cds_start": 497,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000679836.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288695",
"gene_hgnc_id": null,
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu",
"transcript": "ENST00000680700.1",
"protein_id": "ENSP00000504926.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 236,
"cds_start": 497,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000680700.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.362G>A",
"hgvs_p": "p.Gly121Glu",
"transcript": "XM_017008601.2",
"protein_id": "XP_016864090.1",
"transcript_support_level": null,
"aa_start": 121,
"aa_end": null,
"aa_length": 273,
"cds_start": 362,
"cds_end": null,
"cds_length": 822,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008601.2"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.365-3382G>A",
"hgvs_p": null,
"transcript": "ENST00000870317.1",
"protein_id": "ENSP00000540376.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 252,
"cds_start": null,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000870317.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.289+4718G>A",
"hgvs_p": null,
"transcript": "ENST00000505210.1",
"protein_id": "ENSP00000424714.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 182,
"cds_start": null,
"cds_end": null,
"cds_length": 549,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000505210.1"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "c.364+4718G>A",
"hgvs_p": null,
"transcript": "XM_005265767.4",
"protein_id": "XP_005265824.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 207,
"cds_start": null,
"cds_end": null,
"cds_length": 624,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265767.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "n.506G>A",
"hgvs_p": null,
"transcript": "ENST00000514398.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000514398.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "n.*103G>A",
"hgvs_p": null,
"transcript": "ENST00000677177.2",
"protein_id": "ENSP00000504451.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000677177.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "n.369G>A",
"hgvs_p": null,
"transcript": "ENST00000677217.1",
"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": "retained_intron",
"feature": "ENST00000677217.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "n.394G>A",
"hgvs_p": null,
"transcript": "ENST00000678717.1",
"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": "ENST00000678717.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288695",
"gene_hgnc_id": null,
"hgvs_c": "n.*103G>A",
"hgvs_p": null,
"transcript": "ENST00000679351.1",
"protein_id": "ENSP00000505676.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000679351.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"hgvs_c": "n.*103G>A",
"hgvs_p": null,
"transcript": "ENST00000677177.2",
"protein_id": "ENSP00000504451.2",
"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": "nonsense_mediated_decay",
"feature": "ENST00000677177.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000288695",
"gene_hgnc_id": null,
"hgvs_c": "n.*103G>A",
"hgvs_p": null,
"transcript": "ENST00000679351.1",
"protein_id": "ENSP00000505676.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000679351.1"
}
],
"gene_symbol": "SRD5A3",
"gene_hgnc_id": 25812,
"dbsnp": "rs879845715",
"frequency_reference_population": 0.000009294129,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.00000957664,
"gnomad_genomes_af": 0.00000657756,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9706788063049316,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.779,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8372,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.27,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.867,
"phylop100way_prediction": "Pathogenic",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_024592.5",
"gene_symbol": "SRD5A3",
"hgnc_id": 25812,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000679707.1",
"gene_symbol": "ENSG00000288695",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.497G>A",
"hgvs_p": "p.Gly166Glu"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000433175.6",
"gene_symbol": "SRD5A3-AS1",
"hgnc_id": 44138,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1382C>T",
"hgvs_p": null
}
],
"clinvar_disease": "SRD5A3-congenital disorder of glycosylation",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "SRD5A3-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}