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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: 10-73124319-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=73124319&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 73124319,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_015901.6",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "NM_015901.6",
"protein_id": "NP_056985.3",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 352,
"cds_start": 464,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000357321.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015901.6"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "ENST00000357321.9",
"protein_id": "ENSP00000349874.4",
"transcript_support_level": 5,
"aa_start": 155,
"aa_end": null,
"aa_length": 352,
"cds_start": 464,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015901.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357321.9"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "ENST00000349051.9",
"protein_id": "ENSP00000335326.6",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 263,
"cds_start": 464,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000349051.9"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "ENST00000372997.3",
"protein_id": "ENSP00000362088.3",
"transcript_support_level": 1,
"aa_start": 155,
"aa_end": null,
"aa_length": 235,
"cds_start": 464,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000372997.3"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "ENST00000617744.5",
"protein_id": "ENSP00000484185.2",
"transcript_support_level": 5,
"aa_start": 155,
"aa_end": null,
"aa_length": 352,
"cds_start": 464,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000617744.5"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "ENST00000898515.1",
"protein_id": "ENSP00000568574.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 352,
"cds_start": 464,
"cds_end": null,
"cds_length": 1059,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000898515.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "NM_001283014.2",
"protein_id": "NP_001269943.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 263,
"cds_start": 464,
"cds_end": null,
"cds_length": 792,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001283014.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.437C>T",
"hgvs_p": "p.Thr146Met",
"transcript": "ENST00000972079.1",
"protein_id": "ENSP00000642138.1",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 254,
"cds_start": 437,
"cds_end": null,
"cds_length": 765,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000972079.1"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "NM_001283015.2",
"protein_id": "NP_001269944.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 235,
"cds_start": 464,
"cds_end": null,
"cds_length": 708,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001283015.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.86C>T",
"hgvs_p": "p.Thr29Met",
"transcript": "NM_001283016.2",
"protein_id": "NP_001269945.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 226,
"cds_start": 86,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001283016.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.86C>T",
"hgvs_p": "p.Thr29Met",
"transcript": "XM_024447926.2",
"protein_id": "XP_024303694.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 226,
"cds_start": 86,
"cds_end": null,
"cds_length": 681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024447926.2"
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met",
"transcript": "XM_047424984.1",
"protein_id": "XP_047280940.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 202,
"cds_start": 464,
"cds_end": null,
"cds_length": 609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424984.1"
},
{
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.-126-799C>T",
"hgvs_p": null,
"transcript": "NM_001283017.2",
"protein_id": "NP_001269946.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": null,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001283017.2"
},
{
"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": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.-126-799C>T",
"hgvs_p": null,
"transcript": "NM_001283019.2",
"protein_id": "NP_001269948.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": null,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001283019.2"
},
{
"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": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.-389-799C>T",
"hgvs_p": null,
"transcript": "ENST00000537969.6",
"protein_id": "ENSP00000438223.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": null,
"cds_end": null,
"cds_length": 243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000537969.6"
},
{
"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": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "c.-126-799C>T",
"hgvs_p": null,
"transcript": "XM_047424985.1",
"protein_id": "XP_047280941.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": null,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424985.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "n.464C>T",
"hgvs_p": null,
"transcript": "ENST00000488223.6",
"protein_id": "ENSP00000521046.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000488223.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "n.86C>T",
"hgvs_p": null,
"transcript": "ENST00000544879.6",
"protein_id": "ENSP00000440760.2",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000544879.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "n.586C>T",
"hgvs_p": null,
"transcript": "NR_104264.2",
"protein_id": null,
"transcript_support_level": null,
"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": "NR_104264.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"hgvs_c": "n.509-799C>T",
"hgvs_p": null,
"transcript": "ENST00000850962.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000850962.1"
}
],
"gene_symbol": "NUDT13",
"gene_hgnc_id": 18827,
"dbsnp": "rs200833463",
"frequency_reference_population": 0.00019107803,
"hom_count_reference_population": 0,
"allele_count_reference_population": 306,
"gnomad_exomes_af": 0.000194596,
"gnomad_genomes_af": 0.000157602,
"gnomad_exomes_ac": 282,
"gnomad_genomes_ac": 24,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.24937182664871216,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.4099999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.134,
"revel_prediction": "Benign",
"alphamissense_score": 0.0744,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.075,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.18,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.34354191988729,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_015901.6",
"gene_symbol": "NUDT13",
"hgnc_id": 18827,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.464C>T",
"hgvs_p": "p.Thr155Met"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}