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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: 9-84285439-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=84285439&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 84285439,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_022127.3",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.1553A>G",
"hgvs_p": "p.Asn518Ser",
"transcript": "NM_001199633.2",
"protein_id": "NP_001186562.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 691,
"cds_start": 1553,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 1678,
"cdna_end": null,
"cdna_length": 4962,
"mane_select": "ENST00000376238.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001199633.2"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.1553A>G",
"hgvs_p": "p.Asn518Ser",
"transcript": "ENST00000376238.5",
"protein_id": "ENSP00000365413.4",
"transcript_support_level": 1,
"aa_start": 518,
"aa_end": null,
"aa_length": 691,
"cds_start": 1553,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 1678,
"cdna_end": null,
"cdna_length": 4962,
"mane_select": "NM_001199633.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000376238.5"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.1553A>G",
"hgvs_p": "p.Asn518Ser",
"transcript": "NM_022127.3",
"protein_id": "NP_071410.1",
"transcript_support_level": null,
"aa_start": 518,
"aa_end": null,
"aa_length": 691,
"cds_start": 1553,
"cds_end": null,
"cds_length": 2076,
"cdna_start": 1874,
"cdna_end": null,
"cdna_length": 5158,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022127.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.1637A>G",
"hgvs_p": "p.Asn546Ser",
"transcript": "XM_011518905.3",
"protein_id": "XP_011517207.1",
"transcript_support_level": null,
"aa_start": 546,
"aa_end": null,
"aa_length": 719,
"cds_start": 1637,
"cds_end": null,
"cds_length": 2160,
"cdna_start": 1762,
"cdna_end": null,
"cdna_length": 5046,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518905.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.1637A>G",
"hgvs_p": "p.Asn546Ser",
"transcript": "XM_011518906.3",
"protein_id": "XP_011517208.1",
"transcript_support_level": null,
"aa_start": 546,
"aa_end": null,
"aa_length": 719,
"cds_start": 1637,
"cds_end": null,
"cds_length": 2160,
"cdna_start": 1958,
"cdna_end": null,
"cdna_length": 5242,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518906.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.1304A>G",
"hgvs_p": "p.Asn435Ser",
"transcript": "XM_011518907.3",
"protein_id": "XP_011517209.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 608,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1827,
"cdna_start": 1677,
"cdna_end": null,
"cdna_length": 4961,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518907.3"
},
{
"aa_ref": "N",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.914A>G",
"hgvs_p": "p.Asn305Ser",
"transcript": "XM_011518908.3",
"protein_id": "XP_011517210.1",
"transcript_support_level": null,
"aa_start": 305,
"aa_end": null,
"aa_length": 478,
"cds_start": 914,
"cds_end": null,
"cds_length": 1437,
"cdna_start": 1600,
"cdna_end": null,
"cdna_length": 4884,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011518908.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "n.1854A>G",
"hgvs_p": null,
"transcript": "NR_037638.3",
"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": 5138,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_037638.3"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC28A3-AS1",
"gene_hgnc_id": 55460,
"hgvs_c": "n.182-4501T>C",
"hgvs_p": null,
"transcript": "ENST00000419815.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 373,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000419815.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC28A3-AS1",
"gene_hgnc_id": 55460,
"hgvs_c": "n.231-4501T>C",
"hgvs_p": null,
"transcript": "XR_001746802.1",
"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": 427,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_001746802.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"hgvs_c": "c.*126A>G",
"hgvs_p": null,
"transcript": "XM_047423712.1",
"protein_id": "XP_047279668.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 496,
"cds_start": null,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047423712.1"
}
],
"gene_symbol": "SLC28A3",
"gene_hgnc_id": 16484,
"dbsnp": "rs561817778",
"frequency_reference_population": 0.000054516237,
"hom_count_reference_population": 0,
"allele_count_reference_population": 88,
"gnomad_exomes_af": 0.0000533561,
"gnomad_genomes_af": 0.0000656504,
"gnomad_exomes_ac": 78,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.932442307472229,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.254,
"revel_prediction": "Benign",
"alphamissense_score": 0.1565,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.179,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Moderate",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_022127.3",
"gene_symbol": "SLC28A3",
"hgnc_id": 16484,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1553A>G",
"hgvs_p": "p.Asn518Ser"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000419815.1",
"gene_symbol": "SLC28A3-AS1",
"hgnc_id": 55460,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.182-4501T>C",
"hgvs_p": null
}
],
"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
}