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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: 4-139889909-TTGCTGCTGC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=139889909&ref=TTGCTGCTGC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 139889909,
"ref": "TTGCTGCTGC",
"alt": "T",
"effect": "disruptive_inframe_deletion",
"transcript": "NM_018717.5",
"consequences": [
{
"aa_ref": "QQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAML3",
"gene_hgnc_id": 16272,
"hgvs_c": "c.1518_1526delGCAGCAGCA",
"hgvs_p": "p.Gln507_Gln509del",
"transcript": "NM_018717.5",
"protein_id": "NP_061187.3",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 1138,
"cds_start": 1518,
"cds_end": null,
"cds_length": 3417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000509479.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018717.5"
},
{
"aa_ref": "QQQQ",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAML3",
"gene_hgnc_id": 16272,
"hgvs_c": "c.1518_1526delGCAGCAGCA",
"hgvs_p": "p.Gln507_Gln509del",
"transcript": "ENST00000509479.6",
"protein_id": "ENSP00000421180.1",
"transcript_support_level": 1,
"aa_start": 506,
"aa_end": null,
"aa_length": 1138,
"cds_start": 1518,
"cds_end": null,
"cds_length": 3417,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018717.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000509479.6"
},
{
"aa_ref": "QQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAML3",
"gene_hgnc_id": 16272,
"hgvs_c": "c.1518_1526delGCAGCAGCA",
"hgvs_p": "p.Gln507_Gln509del",
"transcript": "ENST00000899537.1",
"protein_id": "ENSP00000569596.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 1137,
"cds_start": 1518,
"cds_end": null,
"cds_length": 3414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000899537.1"
},
{
"aa_ref": "QQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAML3",
"gene_hgnc_id": 16272,
"hgvs_c": "c.1518_1526delGCAGCAGCA",
"hgvs_p": "p.Gln507_Gln509del",
"transcript": "XM_047415929.1",
"protein_id": "XP_047271885.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 1137,
"cds_start": 1518,
"cds_end": null,
"cds_length": 3414,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047415929.1"
},
{
"aa_ref": "QQQQ",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"disruptive_inframe_deletion"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MAML3",
"gene_hgnc_id": 16272,
"hgvs_c": "c.1518_1526delGCAGCAGCA",
"hgvs_p": "p.Gln507_Gln509del",
"transcript": "XM_047415930.1",
"protein_id": "XP_047271886.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 746,
"cds_start": 1518,
"cds_end": null,
"cds_length": 2241,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047415930.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MAML3",
"gene_hgnc_id": 16272,
"hgvs_c": "c.109-159251_109-159243delGCAGCAGCA",
"hgvs_p": null,
"transcript": "ENST00000502696.1",
"protein_id": "ENSP00000422783.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 184,
"cds_start": null,
"cds_end": null,
"cds_length": 557,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000502696.1"
},
{
"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": "ENSG00000294637",
"gene_hgnc_id": null,
"hgvs_c": "n.183-6480_183-6472delCTGCTGCTG",
"hgvs_p": null,
"transcript": "ENST00000724876.1",
"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": "ENST00000724876.1"
},
{
"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": "ENSG00000294637",
"gene_hgnc_id": null,
"hgvs_c": "n.308+1546_308+1554delCTGCTGCTG",
"hgvs_p": null,
"transcript": "ENST00000724877.1",
"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": "ENST00000724877.1"
}
],
"gene_symbol": "MAML3",
"gene_hgnc_id": 16272,
"dbsnp": "rs58015886",
"frequency_reference_population": 0.0070667835,
"hom_count_reference_population": 339,
"allele_count_reference_population": 10424,
"gnomad_exomes_af": 0.00471393,
"gnomad_genomes_af": 0.077306,
"gnomad_exomes_ac": 6728,
"gnomad_genomes_ac": 3696,
"gnomad_exomes_homalt": 201,
"gnomad_genomes_homalt": 138,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 4.001,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP3,BA1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP3",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_018717.5",
"gene_symbol": "MAML3",
"hgnc_id": 16272,
"effects": [
"disruptive_inframe_deletion"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1518_1526delGCAGCAGCA",
"hgvs_p": "p.Gln507_Gln509del"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000724876.1",
"gene_symbol": "ENSG00000294637",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.183-6480_183-6472delCTGCTGCTG",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}