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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: 1-23798160-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=23798160&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 23798160,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000617979.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly",
"transcript": "NM_001008216.2",
"protein_id": "NP_001008217.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 348,
"cds_start": 308,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 427,
"cdna_end": null,
"cdna_length": 1516,
"mane_select": "ENST00000617979.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly",
"transcript": "ENST00000617979.5",
"protein_id": "ENSP00000483375.1",
"transcript_support_level": 1,
"aa_start": 103,
"aa_end": null,
"aa_length": 348,
"cds_start": 308,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 427,
"cdna_end": null,
"cdna_length": 1516,
"mane_select": "NM_001008216.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly",
"transcript": "ENST00000374497.7",
"protein_id": "ENSP00000363621.3",
"transcript_support_level": 1,
"aa_start": 103,
"aa_end": null,
"aa_length": 348,
"cds_start": 308,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 400,
"cdna_end": null,
"cdna_length": 1488,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly",
"transcript": "NM_000403.4",
"protein_id": "NP_000394.2",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 348,
"cds_start": 308,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 576,
"cdna_end": null,
"cdna_length": 1665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly",
"transcript": "NM_001127621.2",
"protein_id": "NP_001121093.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 348,
"cds_start": 308,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 495,
"cdna_end": null,
"cdna_length": 1584,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asp39Gly",
"transcript": "ENST00000429356.5",
"protein_id": "ENSP00000398585.1",
"transcript_support_level": 5,
"aa_start": 39,
"aa_end": null,
"aa_length": 238,
"cds_start": 116,
"cds_end": null,
"cds_length": 718,
"cdna_start": 355,
"cdna_end": null,
"cdna_length": 957,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.116A>G",
"hgvs_p": "p.Asp39Gly",
"transcript": "ENST00000418277.5",
"protein_id": "ENSP00000414719.1",
"transcript_support_level": 5,
"aa_start": 39,
"aa_end": null,
"aa_length": 226,
"cds_start": 116,
"cds_end": null,
"cds_length": 681,
"cdna_start": 317,
"cdna_end": null,
"cdna_length": 882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly",
"transcript": "ENST00000425913.5",
"protein_id": "ENSP00000393359.1",
"transcript_support_level": 5,
"aa_start": 103,
"aa_end": null,
"aa_length": 193,
"cds_start": 308,
"cds_end": null,
"cds_length": 584,
"cdna_start": 600,
"cdna_end": null,
"cdna_length": 876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly",
"transcript": "ENST00000445705.1",
"protein_id": "ENSP00000398257.1",
"transcript_support_level": 2,
"aa_start": 103,
"aa_end": null,
"aa_length": 193,
"cds_start": 308,
"cds_end": null,
"cds_length": 582,
"cdna_start": 518,
"cdna_end": null,
"cdna_length": 792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "n.426A>G",
"hgvs_p": null,
"transcript": "ENST00000459934.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1563,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "n.768A>G",
"hgvs_p": null,
"transcript": "ENST00000467493.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 987,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "n.253A>G",
"hgvs_p": null,
"transcript": "ENST00000470949.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "n.712A>G",
"hgvs_p": null,
"transcript": "ENST00000481736.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1801,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "n.409A>G",
"hgvs_p": null,
"transcript": "ENST00000486382.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "n.*220A>G",
"hgvs_p": null,
"transcript": "ENST00000466250.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 598,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"hgvs_c": "n.*167A>G",
"hgvs_p": null,
"transcript": "ENST00000470383.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GALE",
"gene_hgnc_id": 4116,
"dbsnp": "rs28940883",
"frequency_reference_population": 0.0000020522082,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205221,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.583175539970398,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.671,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1549,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.14,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.027,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP2",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000617979.5",
"gene_symbol": "GALE",
"hgnc_id": 4116,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.308A>G",
"hgvs_p": "p.Asp103Gly"
}
],
"clinvar_disease": "UDPglucose-4-epimerase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "UDPglucose-4-epimerase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}