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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: 2-165748797-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=165748797&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 165748797,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_004482.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "NM_004482.4",
"protein_id": "NP_004473.2",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000392701.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004482.4"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "ENST00000392701.8",
"protein_id": "ENSP00000376465.3",
"transcript_support_level": 1,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004482.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392701.8"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1100T>G",
"hgvs_p": "p.Leu367Arg",
"transcript": "ENST00000409882.5",
"protein_id": "ENSP00000386955.1",
"transcript_support_level": 1,
"aa_start": 367,
"aa_end": null,
"aa_length": 371,
"cds_start": 1100,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409882.5"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1946T>G",
"hgvs_p": "p.Leu649Arg",
"transcript": "ENST00000902717.1",
"protein_id": "ENSP00000572776.1",
"transcript_support_level": null,
"aa_start": 649,
"aa_end": null,
"aa_length": 653,
"cds_start": 1946,
"cds_end": null,
"cds_length": 1962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902717.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "ENST00000715282.1",
"protein_id": "ENSP00000520447.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000715282.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "ENST00000902718.1",
"protein_id": "ENSP00000572777.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902718.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "ENST00000916822.1",
"protein_id": "ENSP00000586881.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916822.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "ENST00000916823.1",
"protein_id": "ENSP00000586882.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916823.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "ENST00000916824.1",
"protein_id": "ENSP00000586883.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916824.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "ENST00000970388.1",
"protein_id": "ENSP00000640447.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970388.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1784T>G",
"hgvs_p": "p.Leu595Arg",
"transcript": "ENST00000902715.1",
"protein_id": "ENSP00000572774.1",
"transcript_support_level": null,
"aa_start": 595,
"aa_end": null,
"aa_length": 599,
"cds_start": 1784,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902715.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1685T>G",
"hgvs_p": "p.Leu562Arg",
"transcript": "ENST00000902716.1",
"protein_id": "ENSP00000572775.1",
"transcript_support_level": null,
"aa_start": 562,
"aa_end": null,
"aa_length": 566,
"cds_start": 1685,
"cds_end": null,
"cds_length": 1701,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000902716.1"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "XM_005246449.2",
"protein_id": "XP_005246506.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005246449.2"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "XM_011510929.2",
"protein_id": "XP_011509231.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510929.2"
},
{
"aa_ref": "L",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg",
"transcript": "XM_017003770.2",
"protein_id": "XP_016859259.1",
"transcript_support_level": null,
"aa_start": 629,
"aa_end": null,
"aa_length": 633,
"cds_start": 1886,
"cds_end": null,
"cds_length": 1902,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017003770.2"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000307262",
"gene_hgnc_id": null,
"hgvs_c": "n.131-1000A>C",
"hgvs_p": null,
"transcript": "ENST00000824811.1",
"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": "ENST00000824811.1"
}
],
"gene_symbol": "GALNT3",
"gene_hgnc_id": 4125,
"dbsnp": "rs755865415",
"frequency_reference_population": 6.853887e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.85389e-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": 0.32313334941864014,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.496,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3439,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.315,
"phylop100way_prediction": "Pathogenic",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004482.4",
"gene_symbol": "GALNT3",
"hgnc_id": 4125,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1886T>G",
"hgvs_p": "p.Leu629Arg"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000824811.1",
"gene_symbol": "ENSG00000307262",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.131-1000A>C",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}