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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: 1-97373560-CCTGCCCACAGGCCAGG-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=97373560&ref=CCTGCCCACAGGCCAGG&alt=C&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"effects": [
"frameshift_variant",
"splice_region_variant"
],
"gene_symbol": "DPYD",
"hgnc_id": 3012,
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"inheritance_mode": "AR",
"pathogenic_score": 16,
"score": 16,
"transcript": "NM_000110.4",
"verdict": "Pathogenic"
},
{
"benign_score": 0,
"criteria": [
"PP3",
"PP5_Very_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC105378867",
"hgnc_id": null,
"hgvs_c": "n.4217+6361_4217+6376delTGCCCACAGGCCAGGC",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 9,
"score": 9,
"transcript": "XR_007066236.1",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_score": 16,
"allele_count_reference_population": 91,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "C",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "1",
"clinvar_classification": "Likely pathogenic",
"clinvar_disease": "Dihydropyrimidine dehydrogenase deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LP:6",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1025,
"aa_ref": "GLACGQ",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 2170,
"cds_end": null,
"cds_length": 3078,
"cds_start": 2043,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 23,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_000110.4",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370192.8",
"protein_coding": true,
"protein_id": "NP_000101.2",
"strand": false,
"transcript": "NM_000110.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1025,
"aa_ref": "GLACGQ",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4423,
"cdna_start": 2170,
"cds_end": null,
"cds_length": 3078,
"cds_start": 2043,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 23,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000370192.8",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000110.4",
"protein_coding": true,
"protein_id": "ENSP00000359211.3",
"strand": false,
"transcript": "ENST00000370192.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1081,
"aa_ref": "GLACGQ",
"aa_start": 737,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4583,
"cdna_start": 2333,
"cds_end": null,
"cds_length": 3246,
"cds_start": 2211,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 24,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000876340.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2211_2226delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu738fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546399.1",
"strand": false,
"transcript": "ENST00000876340.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1060,
"aa_ref": "GLACGQ",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4525,
"cdna_start": 2170,
"cds_end": null,
"cds_length": 3183,
"cds_start": 2043,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 24,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000969915.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639974.1",
"strand": false,
"transcript": "ENST00000969915.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1058,
"aa_ref": "GLACGQ",
"aa_start": 714,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4528,
"cdna_start": 2275,
"cds_end": null,
"cds_length": 3177,
"cds_start": 2142,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 24,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000876335.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2142_2157delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu715fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546394.1",
"strand": false,
"transcript": "ENST00000876335.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1055,
"aa_ref": "GLACGQ",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4527,
"cdna_start": 2188,
"cds_end": null,
"cds_length": 3168,
"cds_start": 2043,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 24,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000969914.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000639973.1",
"strand": false,
"transcript": "ENST00000969914.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1002,
"aa_ref": "GLACGQ",
"aa_start": 658,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4374,
"cdna_start": 2124,
"cds_end": null,
"cds_length": 3009,
"cds_start": 1974,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 22,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000876334.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1974_1989delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu659fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546393.1",
"strand": false,
"transcript": "ENST00000876334.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 993,
"aa_ref": "GLACGQ",
"aa_start": 649,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4254,
"cdna_start": 2001,
"cds_end": null,
"cds_length": 2982,
"cds_start": 1947,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 23,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000876341.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1947_1962delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu650fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546400.1",
"strand": false,
"transcript": "ENST00000876341.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 988,
"aa_ref": "GLACGQ",
"aa_start": 644,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4307,
"cdna_start": 2054,
"cds_end": null,
"cds_length": 2967,
"cds_start": 1932,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 22,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000876339.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1932_1947delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu645fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546398.1",
"strand": false,
"transcript": "ENST00000876339.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 985,
"aa_ref": "GLACGQ",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4303,
"cdna_start": 2170,
"cds_end": null,
"cds_length": 2958,
"cds_start": 2043,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 22,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000876337.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546396.1",
"strand": false,
"transcript": "ENST00000876337.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 978,
"aa_ref": "GLACGQ",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4282,
"cdna_start": 2170,
"cds_end": null,
"cds_length": 2937,
"cds_start": 2043,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 22,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000876336.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546395.1",
"strand": false,
"transcript": "ENST00000876336.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 953,
"aa_ref": "GLACGQ",
"aa_start": 609,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4207,
"cdna_start": 1954,
"cds_end": null,
"cds_length": 2862,
"cds_start": 1827,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 22,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000876338.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1827_1842delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu610fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000546397.1",
"strand": false,
"transcript": "ENST00000876338.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 988,
"aa_ref": "GLACGQ",
"aa_start": 644,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4337,
"cdna_start": 2084,
"cds_end": null,
"cds_length": 2967,
"cds_start": 1932,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 22,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_017000507.2",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1932_1947delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu645fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016855996.1",
"strand": false,
"transcript": "XM_017000507.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 953,
"aa_ref": "GLACGQ",
"aa_start": 609,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4232,
"cdna_start": 1979,
"cds_end": null,
"cds_length": 2862,
"cds_start": 1827,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 22,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_005270562.3",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1827_1842delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu610fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005270619.2",
"strand": false,
"transcript": "XM_005270562.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 949,
"aa_ref": "GLACGQ",
"aa_start": 605,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4341,
"cdna_start": 2088,
"cds_end": null,
"cds_length": 2850,
"cds_start": 1815,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 23,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047448076.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1815_1830delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu606fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304032.1",
"strand": false,
"transcript": "XM_047448076.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 916,
"aa_ref": "GLACGQ",
"aa_start": 572,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4121,
"cdna_start": 1868,
"cds_end": null,
"cds_length": 2751,
"cds_start": 1716,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 21,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_047448077.1",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.1716_1731delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu573fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047304033.1",
"strand": false,
"transcript": "XM_047448077.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 889,
"aa_ref": "GLACGQ",
"aa_start": 681,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3097,
"cdna_start": 2195,
"cds_end": null,
"cds_length": 2670,
"cds_start": 2043,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_count": 21,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_006710397.4",
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"hgvs_c": "c.2043_2058delCCTGGCCTGTGGGCAG",
"hgvs_p": "p.Leu682fs",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006710460.1",
"strand": false,
"transcript": "XM_006710397.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5287,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007066236.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC105378867",
"hgvs_c": "n.4217+6361_4217+6376delTGCCCACAGGCCAGGC",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007066236.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4436,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_007066237.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC105378867",
"hgvs_c": "n.4217+6361_4217+6376delTGCCCACAGGCCAGGC",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "XR_007066237.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs773499329",
"effect": "frameshift_variant,splice_region_variant",
"frequency_reference_population": 0.00005639494,
"gene_hgnc_id": 3012,
"gene_symbol": "DPYD",
"gnomad_exomes_ac": 86,
"gnomad_exomes_af": 0.0000588502,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328338,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely pathogenic",
"phenotype_combined": "Dihydropyrimidine dehydrogenase deficiency|not provided",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 9.049,
"pos": 97373560,
"ref": "CCTGCCCACAGGCCAGG",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_000110.4"
}
]
}