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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: 1-185120198-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=185120198&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 185120198,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_030934.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.2023G>A",
"hgvs_p": "p.Val675Ile",
"transcript": "NM_030934.5",
"protein_id": "NP_112196.3",
"transcript_support_level": null,
"aa_start": 675,
"aa_end": null,
"aa_length": 733,
"cds_start": 2023,
"cds_end": null,
"cds_length": 2202,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000367506.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_030934.5"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.2023G>A",
"hgvs_p": "p.Val675Ile",
"transcript": "ENST00000367506.10",
"protein_id": "ENSP00000356476.5",
"transcript_support_level": 1,
"aa_start": 675,
"aa_end": null,
"aa_length": 733,
"cds_start": 2023,
"cds_end": null,
"cds_length": 2202,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_030934.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000367506.10"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.2086G>A",
"hgvs_p": "p.Val696Ile",
"transcript": "ENST00000942796.1",
"protein_id": "ENSP00000612855.1",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 754,
"cds_start": 2086,
"cds_end": null,
"cds_length": 2265,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000942796.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.2020G>A",
"hgvs_p": "p.Val674Ile",
"transcript": "ENST00000860207.1",
"protein_id": "ENSP00000530266.1",
"transcript_support_level": null,
"aa_start": 674,
"aa_end": null,
"aa_length": 732,
"cds_start": 2020,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860207.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1981G>A",
"hgvs_p": "p.Val661Ile",
"transcript": "ENST00000913482.1",
"protein_id": "ENSP00000583541.1",
"transcript_support_level": null,
"aa_start": 661,
"aa_end": null,
"aa_length": 719,
"cds_start": 1981,
"cds_end": null,
"cds_length": 2160,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913482.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1960G>A",
"hgvs_p": "p.Val654Ile",
"transcript": "ENST00000860206.1",
"protein_id": "ENSP00000530265.1",
"transcript_support_level": null,
"aa_start": 654,
"aa_end": null,
"aa_length": 712,
"cds_start": 1960,
"cds_end": null,
"cds_length": 2139,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860206.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1912G>A",
"hgvs_p": "p.Val638Ile",
"transcript": "ENST00000913481.1",
"protein_id": "ENSP00000583540.1",
"transcript_support_level": null,
"aa_start": 638,
"aa_end": null,
"aa_length": 696,
"cds_start": 1912,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000913481.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1810G>A",
"hgvs_p": "p.Val604Ile",
"transcript": "ENST00000860209.1",
"protein_id": "ENSP00000530268.1",
"transcript_support_level": null,
"aa_start": 604,
"aa_end": null,
"aa_length": 662,
"cds_start": 1810,
"cds_end": null,
"cds_length": 1989,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860209.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1555G>A",
"hgvs_p": "p.Val519Ile",
"transcript": "NM_001202423.2",
"protein_id": "NP_001189352.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 577,
"cds_start": 1555,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001202423.2"
},
{
"aa_ref": "V",
"aa_alt": "I",
"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": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1369G>A",
"hgvs_p": "p.Val457Ile",
"transcript": "ENST00000860208.1",
"protein_id": "ENSP00000530267.1",
"transcript_support_level": null,
"aa_start": 457,
"aa_end": null,
"aa_length": 515,
"cds_start": 1369,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860208.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1555G>A",
"hgvs_p": "p.Val519Ile",
"transcript": "XM_047431291.1",
"protein_id": "XP_047287247.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 577,
"cds_start": 1555,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431291.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "c.1555G>A",
"hgvs_p": "p.Val519Ile",
"transcript": "XM_047431292.1",
"protein_id": "XP_047287248.1",
"transcript_support_level": null,
"aa_start": 519,
"aa_end": null,
"aa_length": 577,
"cds_start": 1555,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047431292.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"hgvs_c": "n.561G>A",
"hgvs_p": null,
"transcript": "ENST00000465827.1",
"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": "pseudogene",
"feature": "ENST00000465827.1"
}
],
"gene_symbol": "TRMT1L",
"gene_hgnc_id": 16782,
"dbsnp": "rs1046962945",
"frequency_reference_population": 0.0000055803503,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000547701,
"gnomad_genomes_af": 0.00000657237,
"gnomad_exomes_ac": 8,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11894339323043823,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.042,
"revel_prediction": "Benign",
"alphamissense_score": 0.0545,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.709,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_030934.5",
"gene_symbol": "TRMT1L",
"hgnc_id": 16782,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2023G>A",
"hgvs_p": "p.Val675Ile"
}
],
"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
}