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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-78124992-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=78124992&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 78124992,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000291.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1055C>A",
"hgvs_p": "p.Thr352Asn",
"transcript": "NM_000291.4",
"protein_id": "NP_000282.1",
"transcript_support_level": null,
"aa_start": 352,
"aa_end": null,
"aa_length": 417,
"cds_start": 1055,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000373316.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000291.4"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1055C>A",
"hgvs_p": "p.Thr352Asn",
"transcript": "ENST00000373316.5",
"protein_id": "ENSP00000362413.4",
"transcript_support_level": 1,
"aa_start": 352,
"aa_end": null,
"aa_length": 417,
"cds_start": 1055,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000291.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373316.5"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1085C>A",
"hgvs_p": "p.Thr362Asn",
"transcript": "ENST00000878879.1",
"protein_id": "ENSP00000548938.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 427,
"cds_start": 1085,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878879.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1085C>A",
"hgvs_p": "p.Thr362Asn",
"transcript": "ENST00000925024.1",
"protein_id": "ENSP00000595083.1",
"transcript_support_level": null,
"aa_start": 362,
"aa_end": null,
"aa_length": 427,
"cds_start": 1085,
"cds_end": null,
"cds_length": 1284,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925024.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1067C>A",
"hgvs_p": "p.Thr356Asn",
"transcript": "ENST00000951220.1",
"protein_id": "ENSP00000621279.1",
"transcript_support_level": null,
"aa_start": 356,
"aa_end": null,
"aa_length": 421,
"cds_start": 1067,
"cds_end": null,
"cds_length": 1266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951220.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1055C>A",
"hgvs_p": "p.Thr352Asn",
"transcript": "ENST00000925019.1",
"protein_id": "ENSP00000595078.1",
"transcript_support_level": null,
"aa_start": 352,
"aa_end": null,
"aa_length": 415,
"cds_start": 1055,
"cds_end": null,
"cds_length": 1248,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925019.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1055C>A",
"hgvs_p": "p.Thr352Asn",
"transcript": "ENST00000925020.1",
"protein_id": "ENSP00000595079.1",
"transcript_support_level": null,
"aa_start": 352,
"aa_end": null,
"aa_length": 414,
"cds_start": 1055,
"cds_end": null,
"cds_length": 1245,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925020.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1037C>A",
"hgvs_p": "p.Thr346Asn",
"transcript": "ENST00000925022.1",
"protein_id": "ENSP00000595081.1",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 411,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1236,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925022.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.1007C>A",
"hgvs_p": "p.Thr336Asn",
"transcript": "ENST00000951221.1",
"protein_id": "ENSP00000621280.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 401,
"cds_start": 1007,
"cds_end": null,
"cds_length": 1206,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951221.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.971C>A",
"hgvs_p": "p.Thr324Asn",
"transcript": "ENST00000644362.1",
"protein_id": "ENSP00000496140.1",
"transcript_support_level": null,
"aa_start": 324,
"aa_end": null,
"aa_length": 389,
"cds_start": 971,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000644362.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.950C>A",
"hgvs_p": "p.Thr317Asn",
"transcript": "ENST00000925021.1",
"protein_id": "ENSP00000595080.1",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 382,
"cds_start": 950,
"cds_end": null,
"cds_length": 1149,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925021.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.935C>A",
"hgvs_p": "p.Thr312Asn",
"transcript": "ENST00000878877.1",
"protein_id": "ENSP00000548936.1",
"transcript_support_level": null,
"aa_start": 312,
"aa_end": null,
"aa_length": 377,
"cds_start": 935,
"cds_end": null,
"cds_length": 1134,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000878877.1"
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "c.899C>A",
"hgvs_p": "p.Thr300Asn",
"transcript": "ENST00000878878.1",
"protein_id": "ENSP00000548937.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 365,
"cds_start": 899,
"cds_end": null,
"cds_length": 1098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"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.500-344C>A",
"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": null,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"hgvs_c": "n.49C>A",
"hgvs_p": null,
"transcript": "ENST00000476531.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000476531.1"
}
],
"gene_symbol": "PGK1",
"gene_hgnc_id": 8896,
"dbsnp": "rs137852530",
"frequency_reference_population": 9.113976e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.11398e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8151310682296753,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.845,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.971,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.24,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.379,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000291.4",
"gene_symbol": "PGK1",
"hgnc_id": 8896,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1055C>A",
"hgvs_p": "p.Thr352Asn"
}
],
"clinvar_disease": "Phosphoglycerate kinase electrophoretic variant PGK II",
"clinvar_classification": "other",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Phosphoglycerate kinase electrophoretic variant PGK II",
"pathogenicity_classification_combined": "other",
"custom_annotations": null
}
],
"message": null
}