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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: 9-6540109-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=6540109&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 6540109,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000170.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.2607C>A",
"hgvs_p": "p.Pro869Pro",
"transcript": "NM_000170.3",
"protein_id": "NP_000161.2",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 1020,
"cds_start": 2607,
"cds_end": null,
"cds_length": 3063,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000321612.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000170.3"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.2607C>A",
"hgvs_p": "p.Pro869Pro",
"transcript": "ENST00000321612.8",
"protein_id": "ENSP00000370737.4",
"transcript_support_level": 1,
"aa_start": 869,
"aa_end": null,
"aa_length": 1020,
"cds_start": 2607,
"cds_end": null,
"cds_length": 3063,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000170.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000321612.8"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.1042C>A",
"hgvs_p": null,
"transcript": "ENST00000638233.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000638233.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.2175C>A",
"hgvs_p": null,
"transcript": "ENST00000639443.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000639443.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.2607C>A",
"hgvs_p": "p.Pro869Pro",
"transcript": "ENST00000920236.1",
"protein_id": "ENSP00000590295.1",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 1059,
"cds_start": 2607,
"cds_end": null,
"cds_length": 3180,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920236.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.2694C>A",
"hgvs_p": "p.Pro898Pro",
"transcript": "ENST00000953081.1",
"protein_id": "ENSP00000623139.1",
"transcript_support_level": null,
"aa_start": 898,
"aa_end": null,
"aa_length": 1049,
"cds_start": 2694,
"cds_end": null,
"cds_length": 3150,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953081.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.2607C>A",
"hgvs_p": "p.Pro869Pro",
"transcript": "ENST00000920237.1",
"protein_id": "ENSP00000590296.1",
"transcript_support_level": null,
"aa_start": 869,
"aa_end": null,
"aa_length": 993,
"cds_start": 2607,
"cds_end": null,
"cds_length": 2982,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920237.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.807C>A",
"hgvs_p": "p.Pro269Pro",
"transcript": "ENST00000638661.1",
"protein_id": "ENSP00000491369.1",
"transcript_support_level": 5,
"aa_start": 269,
"aa_end": null,
"aa_length": 420,
"cds_start": 807,
"cds_end": null,
"cds_length": 1263,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000638661.1"
},
{
"aa_ref": "P",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.309C>A",
"hgvs_p": "p.Pro103Pro",
"transcript": "ENST00000639639.1",
"protein_id": "ENSP00000491312.1",
"transcript_support_level": 3,
"aa_start": 103,
"aa_end": null,
"aa_length": 254,
"cds_start": 309,
"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": "ENST00000639639.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.2570-3873C>A",
"hgvs_p": null,
"transcript": "ENST00000884130.1",
"protein_id": "ENSP00000554189.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 988,
"cds_start": null,
"cds_end": null,
"cds_length": 2967,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000884130.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "c.770-3873C>A",
"hgvs_p": null,
"transcript": "ENST00000639318.1",
"protein_id": "ENSP00000491932.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 388,
"cds_start": null,
"cds_end": null,
"cds_length": 1167,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000639318.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.71C>A",
"hgvs_p": null,
"transcript": "ENST00000477960.1",
"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": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000477960.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.794C>A",
"hgvs_p": null,
"transcript": "ENST00000638694.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000638694.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.2307C>A",
"hgvs_p": null,
"transcript": "ENST00000639364.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000639364.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.1708C>A",
"hgvs_p": null,
"transcript": "ENST00000639461.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000639461.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.2315C>A",
"hgvs_p": null,
"transcript": "ENST00000639954.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000639954.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"hgvs_c": "n.846C>A",
"hgvs_p": null,
"transcript": "ENST00000640505.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000640505.1"
}
],
"gene_symbol": "GLDC",
"gene_hgnc_id": 4313,
"dbsnp": "rs386833565",
"frequency_reference_population": 0.0000669432,
"hom_count_reference_population": 0,
"allele_count_reference_population": 108,
"gnomad_exomes_af": 0.0000650219,
"gnomad_genomes_af": 0.0000853791,
"gnomad_exomes_ac": 95,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.49000000953674316,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.436,
"phylop100way_prediction": "Benign",
"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": "Likely_benign",
"acmg_criteria": "PP5,BP4,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 2,
"pathogenic_score": 1,
"criteria": [
"PP5",
"BP4",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_000170.3",
"gene_symbol": "GLDC",
"hgnc_id": 4313,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.2607C>A",
"hgvs_p": "p.Pro869Pro"
}
],
"clinvar_disease": "GLDC-related disorder,Glycine encephalopathy,Glycine encephalopathy 1",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:3 LP:3 US:1",
"phenotype_combined": "Glycine encephalopathy|Glycine encephalopathy 1|GLDC-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}