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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: 15-42725228-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=42725228&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "CDAN1",
"hgnc_id": 1713,
"hgvs_c": "c.3474A>C",
"hgvs_p": "p.Leu1158Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_138477.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_score": -21,
"allele_count_reference_population": 435954,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "15",
"clinvar_classification": "Benign",
"clinvar_disease": " congenital dyserythropoietic, type 1a, type I,Anemia,Congenital dyserythropoietic anemia,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.49000000953674316,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1227,
"aa_ref": "L",
"aa_start": 1158,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4657,
"cdna_start": 3500,
"cds_end": null,
"cds_length": 3684,
"cds_start": 3474,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "NM_138477.4",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3474A>C",
"hgvs_p": "p.Leu1158Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000356231.4",
"protein_coding": true,
"protein_id": "NP_612486.2",
"strand": false,
"transcript": "NM_138477.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1227,
"aa_ref": "L",
"aa_start": 1158,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4657,
"cdna_start": 3500,
"cds_end": null,
"cds_length": 3684,
"cds_start": 3474,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000356231.4",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3474A>C",
"hgvs_p": "p.Leu1158Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138477.4",
"protein_coding": true,
"protein_id": "ENSP00000348564.3",
"strand": false,
"transcript": "ENST00000356231.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2562,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000562465.5",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "n.*376A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454246.1",
"strand": false,
"transcript": "ENST00000562465.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2562,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000562465.5",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "n.*376A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000454246.1",
"strand": false,
"transcript": "ENST00000562465.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1228,
"aa_ref": "L",
"aa_start": 1159,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4675,
"cdna_start": 3531,
"cds_end": null,
"cds_length": 3687,
"cds_start": 3477,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000913682.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3477A>C",
"hgvs_p": "p.Leu1159Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583741.1",
"strand": false,
"transcript": "ENST00000913682.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1219,
"aa_ref": "L",
"aa_start": 1150,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4610,
"cdna_start": 3471,
"cds_end": null,
"cds_length": 3660,
"cds_start": 3450,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000913683.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3450A>C",
"hgvs_p": "p.Leu1150Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583742.1",
"strand": false,
"transcript": "ENST00000913683.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1213,
"aa_ref": "L",
"aa_start": 1144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4586,
"cdna_start": 3447,
"cds_end": null,
"cds_length": 3642,
"cds_start": 3432,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000913684.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3432A>C",
"hgvs_p": "p.Leu1144Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000583743.1",
"strand": false,
"transcript": "ENST00000913684.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1120,
"aa_ref": "L",
"aa_start": 1051,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4315,
"cdna_start": 3178,
"cds_end": null,
"cds_length": 3363,
"cds_start": 3153,
"consequences": [
"synonymous_variant"
],
"exon_count": 25,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000959718.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3153A>C",
"hgvs_p": "p.Leu1051Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000629777.1",
"strand": false,
"transcript": "ENST00000959718.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1236,
"aa_ref": "L",
"aa_start": 1167,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4684,
"cdna_start": 3527,
"cds_end": null,
"cds_length": 3711,
"cds_start": 3501,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "XM_011521270.3",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3501A>C",
"hgvs_p": "p.Leu1167Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011519572.1",
"strand": false,
"transcript": "XM_011521270.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1235,
"aa_ref": "L",
"aa_start": 1166,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4681,
"cdna_start": 3524,
"cds_end": null,
"cds_length": 3708,
"cds_start": 3498,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "XM_011521271.3",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3498A>C",
"hgvs_p": "p.Leu1166Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011519573.1",
"strand": false,
"transcript": "XM_011521271.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1228,
"aa_ref": "L",
"aa_start": 1159,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4660,
"cdna_start": 3503,
"cds_end": null,
"cds_length": 3687,
"cds_start": 3477,
"consequences": [
"synonymous_variant"
],
"exon_count": 28,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "XM_005254176.6",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.3477A>C",
"hgvs_p": "p.Leu1159Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005254233.1",
"strand": false,
"transcript": "XM_005254176.6",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 891,
"aa_ref": "L",
"aa_start": 822,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3734,
"cdna_start": 2577,
"cds_end": null,
"cds_length": 2676,
"cds_start": 2466,
"consequences": [
"synonymous_variant"
],
"exon_count": 25,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "XM_011521274.3",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.2466A>C",
"hgvs_p": "p.Leu822Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011519576.1",
"strand": false,
"transcript": "XM_011521274.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 891,
"aa_ref": "L",
"aa_start": 822,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3889,
"cdna_start": 2732,
"cds_end": null,
"cds_length": 2676,
"cds_start": 2466,
"consequences": [
"synonymous_variant"
],
"exon_count": 26,
"exon_rank": 25,
"exon_rank_end": null,
"feature": "XM_047432195.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "c.2466A>C",
"hgvs_p": "p.Leu822Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288151.1",
"strand": false,
"transcript": "XM_047432195.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2076,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 1,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000563604.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "n.410A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000563604.1",
"transcript_support_level": 6
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 408,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000565930.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "n.75A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000565930.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3901,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 25,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000643434.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "n.*2541A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494699.1",
"strand": false,
"transcript": "ENST00000643434.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 3901,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 25,
"exon_rank": 24,
"exon_rank_end": null,
"feature": "ENST00000643434.1",
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"hgvs_c": "n.*2541A>C",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494699.1",
"strand": false,
"transcript": "ENST00000643434.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs16957091",
"effect": "synonymous_variant",
"frequency_reference_population": 0.27017945,
"gene_hgnc_id": 1713,
"gene_symbol": "CDAN1",
"gnomad_exomes_ac": 374211,
"gnomad_exomes_af": 0.256049,
"gnomad_exomes_homalt": 57421,
"gnomad_genomes_ac": 61743,
"gnomad_genomes_af": 0.405958,
"gnomad_genomes_homalt": 18329,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 75750,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "Congenital dyserythropoietic anemia, type I|not specified|not provided|Anemia, congenital dyserythropoietic, type 1a",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.474,
"pos": 42725228,
"ref": "T",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_138477.4"
}
]
}