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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: 22-20425397-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=20425397&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 20425397,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_182895.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARF2",
"gene_hgnc_id": 19869,
"hgvs_c": "c.2579G>A",
"hgvs_p": "p.Arg860Lys",
"transcript": "NM_182895.5",
"protein_id": "NP_878315.2",
"transcript_support_level": null,
"aa_start": 860,
"aa_end": null,
"aa_length": 866,
"cds_start": 2579,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2650,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": "ENST00000622235.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARF2",
"gene_hgnc_id": 19869,
"hgvs_c": "c.2579G>A",
"hgvs_p": "p.Arg860Lys",
"transcript": "ENST00000622235.5",
"protein_id": "ENSP00000477564.2",
"transcript_support_level": 1,
"aa_start": 860,
"aa_end": null,
"aa_length": 866,
"cds_start": 2579,
"cds_end": null,
"cds_length": 2601,
"cdna_start": 2650,
"cdna_end": null,
"cdna_length": 3463,
"mane_select": "NM_182895.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARF2",
"gene_hgnc_id": 19869,
"hgvs_c": "c.2594G>A",
"hgvs_p": "p.Arg865Lys",
"transcript": "ENST00000623402.1",
"protein_id": "ENSP00000485276.1",
"transcript_support_level": 1,
"aa_start": 865,
"aa_end": null,
"aa_length": 871,
"cds_start": 2594,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 2666,
"cdna_end": null,
"cdna_length": 3248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARF2",
"gene_hgnc_id": 19869,
"hgvs_c": "c.2594G>A",
"hgvs_p": "p.Arg865Lys",
"transcript": "NM_153334.7",
"protein_id": "NP_699165.3",
"transcript_support_level": null,
"aa_start": 865,
"aa_end": null,
"aa_length": 871,
"cds_start": 2594,
"cds_end": null,
"cds_length": 2616,
"cdna_start": 2665,
"cdna_end": null,
"cdna_length": 3478,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARF2",
"gene_hgnc_id": 19869,
"hgvs_c": "c.2693G>A",
"hgvs_p": "p.Arg898Lys",
"transcript": "XM_047441585.1",
"protein_id": "XP_047297541.1",
"transcript_support_level": null,
"aa_start": 898,
"aa_end": null,
"aa_length": 904,
"cds_start": 2693,
"cds_end": null,
"cds_length": 2715,
"cdna_start": 2764,
"cdna_end": null,
"cdna_length": 3577,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCARF2",
"gene_hgnc_id": 19869,
"hgvs_c": "c.*808G>A",
"hgvs_p": null,
"transcript": "XM_017029065.3",
"protein_id": "XP_016884554.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 617,
"cds_start": -4,
"cds_end": null,
"cds_length": 1854,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3546,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "ENSG00000305663",
"gene_hgnc_id": null,
"hgvs_c": "n.32+16C>T",
"hgvs_p": null,
"transcript": "ENST00000812275.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 573,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000305663",
"gene_hgnc_id": null,
"hgvs_c": "n.35+16C>T",
"hgvs_p": null,
"transcript": "ENST00000812276.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 544,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SCARF2",
"gene_hgnc_id": 19869,
"dbsnp": "rs367657189",
"frequency_reference_population": 0.000058797177,
"hom_count_reference_population": 1,
"allele_count_reference_population": 84,
"gnomad_exomes_af": 0.0000336883,
"gnomad_genomes_af": 0.000269326,
"gnomad_exomes_ac": 43,
"gnomad_genomes_ac": 41,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011383980512619019,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.027,
"revel_prediction": "Benign",
"alphamissense_score": 0.1009,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.59,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.075,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_182895.5",
"gene_symbol": "SCARF2",
"hgnc_id": 19869,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2579G>A",
"hgvs_p": "p.Arg860Lys"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000812275.1",
"gene_symbol": "ENSG00000305663",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.32+16C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}