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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: 6-107210483-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=107210483&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 107210483,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "NM_020381.4",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.964C>T",
"hgvs_p": "p.Gln322*",
"transcript": "NM_020381.4",
"protein_id": "NP_065114.3",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 399,
"cds_start": 964,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 3536,
"mane_select": "ENST00000369037.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.964C>T",
"hgvs_p": "p.Gln322*",
"transcript": "ENST00000369037.9",
"protein_id": "ENSP00000358033.4",
"transcript_support_level": 1,
"aa_start": 322,
"aa_end": null,
"aa_length": 399,
"cds_start": 964,
"cds_end": null,
"cds_length": 1200,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 3536,
"mane_select": "NM_020381.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.139C>T",
"hgvs_p": "p.Gln47*",
"transcript": "ENST00000449027.1",
"protein_id": "ENSP00000392613.1",
"transcript_support_level": 3,
"aa_start": 47,
"aa_end": null,
"aa_length": 79,
"cds_start": 139,
"cds_end": null,
"cds_length": 241,
"cdna_start": 139,
"cdna_end": null,
"cdna_length": 241,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.964C>T",
"hgvs_p": "p.Gln322*",
"transcript": "XM_011535956.4",
"protein_id": "XP_011534258.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 465,
"cds_start": 964,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 3734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.829C>T",
"hgvs_p": "p.Gln277*",
"transcript": "XM_011535958.4",
"protein_id": "XP_011534260.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 420,
"cds_start": 829,
"cds_end": null,
"cds_length": 1263,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 3599,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.964C>T",
"hgvs_p": "p.Gln322*",
"transcript": "XM_017011082.3",
"protein_id": "XP_016866571.1",
"transcript_support_level": null,
"aa_start": 322,
"aa_end": null,
"aa_length": 359,
"cds_start": 964,
"cds_end": null,
"cds_length": 1080,
"cdna_start": 1243,
"cdna_end": null,
"cdna_length": 2872,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.829C>T",
"hgvs_p": "p.Gln277*",
"transcript": "XM_047419097.1",
"protein_id": "XP_047275053.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 354,
"cds_start": 829,
"cds_end": null,
"cds_length": 1065,
"cdna_start": 1108,
"cdna_end": null,
"cdna_length": 3401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.556C>T",
"hgvs_p": "p.Gln186*",
"transcript": "XM_011535960.4",
"protein_id": "XP_011534262.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 329,
"cds_start": 556,
"cds_end": null,
"cds_length": 990,
"cdna_start": 865,
"cdna_end": null,
"cdna_length": 3356,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.706C>T",
"hgvs_p": "p.Gln236*",
"transcript": "XM_047419098.1",
"protein_id": "XP_047275054.1",
"transcript_support_level": null,
"aa_start": 236,
"aa_end": null,
"aa_length": 313,
"cds_start": 706,
"cds_end": null,
"cds_length": 942,
"cdna_start": 912,
"cdna_end": null,
"cdna_length": 3205,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.424C>T",
"hgvs_p": "p.Gln142*",
"transcript": "XM_047419100.1",
"protein_id": "XP_047275056.1",
"transcript_support_level": null,
"aa_start": 142,
"aa_end": null,
"aa_length": 285,
"cds_start": 424,
"cds_end": null,
"cds_length": 858,
"cdna_start": 927,
"cdna_end": null,
"cdna_length": 3418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.876+1626C>T",
"hgvs_p": null,
"transcript": "XM_011535957.4",
"protein_id": "XP_011534259.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 421,
"cds_start": -4,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3602,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.703-16629C>T",
"hgvs_p": null,
"transcript": "XM_047419096.1",
"protein_id": "XP_047275052.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 363,
"cds_start": -4,
"cds_end": null,
"cds_length": 1092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.876+1626C>T",
"hgvs_p": null,
"transcript": "XM_011535959.4",
"protein_id": "XP_011534261.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 355,
"cds_start": -4,
"cds_end": null,
"cds_length": 1068,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3404,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.741+1626C>T",
"hgvs_p": null,
"transcript": "XM_047419099.1",
"protein_id": "XP_047275055.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 310,
"cds_start": -4,
"cds_end": null,
"cds_length": 933,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.703-16629C>T",
"hgvs_p": null,
"transcript": "XM_011535961.4",
"protein_id": "XP_011534263.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 297,
"cds_start": -4,
"cds_end": null,
"cds_length": 894,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"hgvs_c": "c.568-16629C>T",
"hgvs_p": null,
"transcript": "XM_047419101.1",
"protein_id": "XP_047275057.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 252,
"cds_start": -4,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PDSS2",
"gene_hgnc_id": 23041,
"dbsnp": "rs118203955",
"frequency_reference_population": 0.000007458966,
"hom_count_reference_population": 0,
"allele_count_reference_population": 12,
"gnomad_exomes_af": 0.00000755128,
"gnomad_genomes_af": 0.00000657479,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6299999952316284,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.18000000715255737,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.63,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.314,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.18,
"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": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "NM_020381.4",
"gene_symbol": "PDSS2",
"hgnc_id": 23041,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.964C>T",
"hgvs_p": "p.Gln322*"
}
],
"clinvar_disease": " 3, primary,Coenzyme Q10 deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "Coenzyme Q10 deficiency, primary, 3",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}