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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-78123369-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=78123369&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 78123369,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_000291.4",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.931T>C",
"hgvs_p": "p.Trp311Arg",
"transcript": "NM_000291.4",
"protein_id": "NP_000282.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 417,
"cds_start": 931,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 1024,
"cdna_end": null,
"cdna_length": 4812,
"mane_select": "ENST00000373316.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000291.4"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.931T>C",
"hgvs_p": "p.Trp311Arg",
"transcript": "ENST00000373316.5",
"protein_id": "ENSP00000362413.4",
"transcript_support_level": 1,
"aa_start": 311,
"aa_end": null,
"aa_length": 417,
"cds_start": 931,
"cds_end": null,
"cds_length": 1254,
"cdna_start": 1024,
"cdna_end": null,
"cdna_length": 4812,
"mane_select": "NM_000291.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373316.5"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.931T>C",
"hgvs_p": "p.Trp311Arg",
"transcript": "ENST00000878879.1",
"protein_id": "ENSP00000548938.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 427,
"cds_start": 931,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 1024,
"cdna_end": null,
"cdna_length": 1553,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878879.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.961T>C",
"hgvs_p": "p.Trp321Arg",
"transcript": "ENST00000925024.1",
"protein_id": "ENSP00000595083.1",
"transcript_support_level": null,
"aa_start": 321,
"aa_end": null,
"aa_length": 427,
"cds_start": 961,
"cds_end": null,
"cds_length": 1284,
"cdna_start": 1054,
"cdna_end": null,
"cdna_length": 1820,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925024.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.943T>C",
"hgvs_p": "p.Trp315Arg",
"transcript": "ENST00000951220.1",
"protein_id": "ENSP00000621279.1",
"transcript_support_level": null,
"aa_start": 315,
"aa_end": null,
"aa_length": 421,
"cds_start": 943,
"cds_end": null,
"cds_length": 1266,
"cdna_start": 1064,
"cdna_end": null,
"cdna_length": 1821,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951220.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.931T>C",
"hgvs_p": "p.Trp311Arg",
"transcript": "ENST00000925019.1",
"protein_id": "ENSP00000595078.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 415,
"cds_start": 931,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 1077,
"cdna_end": null,
"cdna_length": 2520,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925019.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.931T>C",
"hgvs_p": "p.Trp311Arg",
"transcript": "ENST00000925020.1",
"protein_id": "ENSP00000595079.1",
"transcript_support_level": null,
"aa_start": 311,
"aa_end": null,
"aa_length": 414,
"cds_start": 931,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 1053,
"cdna_end": null,
"cdna_length": 2486,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925020.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.913T>C",
"hgvs_p": "p.Trp305Arg",
"transcript": "ENST00000925022.1",
"protein_id": "ENSP00000595081.1",
"transcript_support_level": null,
"aa_start": 305,
"aa_end": null,
"aa_length": 411,
"cds_start": 913,
"cds_end": null,
"cds_length": 1236,
"cdna_start": 1043,
"cdna_end": null,
"cdna_length": 2394,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925022.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.883T>C",
"hgvs_p": "p.Trp295Arg",
"transcript": "ENST00000951221.1",
"protein_id": "ENSP00000621280.1",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 401,
"cds_start": 883,
"cds_end": null,
"cds_length": 1206,
"cdna_start": 1001,
"cdna_end": null,
"cdna_length": 1757,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951221.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.847T>C",
"hgvs_p": "p.Trp283Arg",
"transcript": "ENST00000644362.1",
"protein_id": "ENSP00000496140.1",
"transcript_support_level": null,
"aa_start": 283,
"aa_end": null,
"aa_length": 389,
"cds_start": 847,
"cds_end": null,
"cds_length": 1170,
"cdna_start": 963,
"cdna_end": null,
"cdna_length": 2405,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644362.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.826T>C",
"hgvs_p": "p.Trp276Arg",
"transcript": "ENST00000925021.1",
"protein_id": "ENSP00000595080.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 382,
"cds_start": 826,
"cds_end": null,
"cds_length": 1149,
"cdna_start": 985,
"cdna_end": null,
"cdna_length": 2308,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925021.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.811T>C",
"hgvs_p": "p.Trp271Arg",
"transcript": "ENST00000878877.1",
"protein_id": "ENSP00000548936.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 377,
"cds_start": 811,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 907,
"cdna_end": null,
"cdna_length": 2225,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878877.1"
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.775T>C",
"hgvs_p": "p.Trp259Arg",
"transcript": "ENST00000878878.1",
"protein_id": "ENSP00000548937.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 365,
"cds_start": 775,
"cds_end": null,
"cds_length": 1098,
"cdna_start": 871,
"cdna_end": null,
"cdna_length": 1637,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878878.1"
},
{
"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": 7,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.500-1967T>C",
"hgvs_p": null,
"transcript": "ENST00000925023.1",
"protein_id": "ENSP00000595082.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 209,
"cds_start": null,
"cds_end": null,
"cds_length": 630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1166,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925023.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"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": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "n.*31T>C",
"hgvs_p": null,
"transcript": "ENST00000474281.1",
"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": 307,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000474281.1"
}
],
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"dbsnp": "rs1443224391",
"frequency_reference_population": 0.0000027518695,
"hom_count_reference_population": 3,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000275187,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9493852853775024,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.863,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9242,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.525,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP3_Strong,BS2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 4,
"pathogenic_score": 6,
"criteria": [
"PM1",
"PP3_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000291.4",
"gene_symbol": "PGK1",
"hgnc_id": 8896,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.931T>C",
"hgvs_p": "p.Trp311Arg"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}