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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: 1-111238844-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=111238844&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 111238844,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004000.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.830C>T",
"hgvs_p": "p.Ser277Phe",
"transcript": "NM_004000.3",
"protein_id": "NP_003991.2",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 390,
"cds_start": 830,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000369748.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004000.3"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.830C>T",
"hgvs_p": "p.Ser277Phe",
"transcript": "ENST00000369748.9",
"protein_id": "ENSP00000358763.4",
"transcript_support_level": 1,
"aa_start": 277,
"aa_end": null,
"aa_length": 390,
"cds_start": 830,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004000.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369748.9"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Ser198Phe",
"transcript": "ENST00000466741.5",
"protein_id": "ENSP00000437086.1",
"transcript_support_level": 1,
"aa_start": 198,
"aa_end": null,
"aa_length": 311,
"cds_start": 593,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000466741.5"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.830C>T",
"hgvs_p": "p.Ser277Phe",
"transcript": "ENST00000445067.6",
"protein_id": "ENSP00000437082.1",
"transcript_support_level": 5,
"aa_start": 277,
"aa_end": null,
"aa_length": 390,
"cds_start": 830,
"cds_end": null,
"cds_length": 1173,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000445067.6"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.827C>T",
"hgvs_p": "p.Ser276Phe",
"transcript": "ENST00000949913.1",
"protein_id": "ENSP00000619972.1",
"transcript_support_level": null,
"aa_start": 276,
"aa_end": null,
"aa_length": 389,
"cds_start": 827,
"cds_end": null,
"cds_length": 1170,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949913.1"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.800C>T",
"hgvs_p": "p.Ser267Phe",
"transcript": "NM_001025197.1",
"protein_id": "NP_001020368.1",
"transcript_support_level": null,
"aa_start": 267,
"aa_end": null,
"aa_length": 380,
"cds_start": 800,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001025197.1"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.800C>T",
"hgvs_p": "p.Ser267Phe",
"transcript": "ENST00000369744.6",
"protein_id": "ENSP00000358759.2",
"transcript_support_level": 5,
"aa_start": 267,
"aa_end": null,
"aa_length": 380,
"cds_start": 800,
"cds_end": null,
"cds_length": 1143,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000369744.6"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.773C>T",
"hgvs_p": "p.Ser258Phe",
"transcript": "ENST00000907889.1",
"protein_id": "ENSP00000577948.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 371,
"cds_start": 773,
"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": "ENST00000907889.1"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.761C>T",
"hgvs_p": "p.Ser254Phe",
"transcript": "ENST00000949914.1",
"protein_id": "ENSP00000619973.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 367,
"cds_start": 761,
"cds_end": null,
"cds_length": 1104,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000949914.1"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Ser198Phe",
"transcript": "NM_001025199.2",
"protein_id": "NP_001020370.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 311,
"cds_start": 593,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001025199.2"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.593C>T",
"hgvs_p": "p.Ser198Phe",
"transcript": "ENST00000524472.5",
"protein_id": "ENSP00000432049.1",
"transcript_support_level": 2,
"aa_start": 198,
"aa_end": null,
"aa_length": 311,
"cds_start": 593,
"cds_end": null,
"cds_length": 936,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000524472.5"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.458C>T",
"hgvs_p": "p.Ser153Phe",
"transcript": "ENST00000533831.6",
"protein_id": "ENSP00000433176.2",
"transcript_support_level": 5,
"aa_start": 153,
"aa_end": null,
"aa_length": 159,
"cds_start": 458,
"cds_end": null,
"cds_length": 480,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000533831.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.298-2483C>T",
"hgvs_p": null,
"transcript": "ENST00000497220.5",
"protein_id": "ENSP00000435250.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 183,
"cds_start": null,
"cds_end": null,
"cds_length": 552,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000497220.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.-83C>T",
"hgvs_p": null,
"transcript": "ENST00000472825.2",
"protein_id": "ENSP00000435935.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 42,
"cds_start": null,
"cds_end": null,
"cds_length": 129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000472825.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"hgvs_c": "c.*85C>T",
"hgvs_p": null,
"transcript": "ENST00000477185.6",
"protein_id": "ENSP00000436272.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 168,
"cds_start": null,
"cds_end": null,
"cds_length": 508,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000477185.6"
}
],
"gene_symbol": "CHI3L2",
"gene_hgnc_id": 1933,
"dbsnp": "rs1659962225",
"frequency_reference_population": 0.0000034209836,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342098,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.40923550724983215,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.192,
"revel_prediction": "Benign",
"alphamissense_score": 0.2965,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.38,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.594,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.1,
"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_004000.3",
"gene_symbol": "CHI3L2",
"hgnc_id": 1933,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.830C>T",
"hgvs_p": "p.Ser277Phe"
}
],
"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
}