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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: 2-20037578-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=20037578&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 20037578,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_014713.5",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.269T>A",
"hgvs_p": "p.Met90Lys",
"transcript": "NM_014713.5",
"protein_id": "NP_055528.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 233,
"cds_start": 269,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000175091.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014713.5"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.269T>A",
"hgvs_p": "p.Met90Lys",
"transcript": "ENST00000175091.5",
"protein_id": "ENSP00000175091.4",
"transcript_support_level": 1,
"aa_start": 90,
"aa_end": null,
"aa_length": 233,
"cds_start": 269,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014713.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000175091.5"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.269T>A",
"hgvs_p": "p.Met90Lys",
"transcript": "ENST00000941941.1",
"protein_id": "ENSP00000612000.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 242,
"cds_start": 269,
"cds_end": null,
"cds_length": 729,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000941941.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.239T>A",
"hgvs_p": "p.Met80Lys",
"transcript": "ENST00000858090.1",
"protein_id": "ENSP00000528149.1",
"transcript_support_level": null,
"aa_start": 80,
"aa_end": null,
"aa_length": 223,
"cds_start": 239,
"cds_end": null,
"cds_length": 672,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858090.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.269T>A",
"hgvs_p": "p.Met90Lys",
"transcript": "ENST00000911490.1",
"protein_id": "ENSP00000581549.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 201,
"cds_start": 269,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911490.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.269T>A",
"hgvs_p": "p.Met90Lys",
"transcript": "ENST00000911489.1",
"protein_id": "ENSP00000581548.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 200,
"cds_start": 269,
"cds_end": null,
"cds_length": 603,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911489.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.161T>A",
"hgvs_p": "p.Met54Lys",
"transcript": "ENST00000858092.1",
"protein_id": "ENSP00000528151.1",
"transcript_support_level": null,
"aa_start": 54,
"aa_end": null,
"aa_length": 197,
"cds_start": 161,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858092.1"
},
{
"aa_ref": "M",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"hgvs_c": "c.269T>A",
"hgvs_p": "p.Met90Lys",
"transcript": "ENST00000858091.1",
"protein_id": "ENSP00000528150.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 192,
"cds_start": 269,
"cds_end": null,
"cds_length": 579,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858091.1"
}
],
"gene_symbol": "LAPTM4A",
"gene_hgnc_id": 6924,
"dbsnp": "rs745313311",
"frequency_reference_population": 0.00001615294,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000137234,
"gnomad_genomes_af": 0.0000394094,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8641729950904846,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05000000074505806,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.294,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8859,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.77,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.05,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014713.5",
"gene_symbol": "LAPTM4A",
"hgnc_id": 6924,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.269T>A",
"hgvs_p": "p.Met90Lys"
}
],
"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
}