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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: 4-51994854-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=51994854&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "LRRC66",
"hgnc_id": 34299,
"hgvs_c": "c.2168G>A",
"hgvs_p": "p.Ser723Asn",
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_001024611.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong",
"acmg_score": -12,
"allele_count_reference_population": 376,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0753,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.87,
"chr": "4",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.022691965103149414,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 880,
"aa_ref": "S",
"aa_start": 723,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3435,
"cdna_start": 2233,
"cds_end": null,
"cds_length": 2643,
"cds_start": 2168,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001024611.3",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.2168G>A",
"hgvs_p": "p.Ser723Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000682860.1",
"protein_coding": true,
"protein_id": "NP_001019782.1",
"strand": false,
"transcript": "NM_001024611.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 880,
"aa_ref": "S",
"aa_start": 723,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3435,
"cdna_start": 2233,
"cds_end": null,
"cds_length": 2643,
"cds_start": 2168,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000682860.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.2168G>A",
"hgvs_p": "p.Ser723Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001024611.3",
"protein_coding": true,
"protein_id": "ENSP00000508002.1",
"strand": false,
"transcript": "ENST00000682860.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 880,
"aa_ref": "S",
"aa_start": 723,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3327,
"cdna_start": 2175,
"cds_end": null,
"cds_length": 2643,
"cds_start": 2168,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000343457.3",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.2168G>A",
"hgvs_p": "p.Ser723Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000341944.3",
"strand": false,
"transcript": "ENST00000343457.3",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 880,
"aa_ref": "S",
"aa_start": 723,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3490,
"cdna_start": 2250,
"cds_end": null,
"cds_length": 2643,
"cds_start": 2168,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000893847.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.2168G>A",
"hgvs_p": "p.Ser723Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563906.1",
"strand": false,
"transcript": "ENST00000893847.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 760,
"aa_ref": "S",
"aa_start": 603,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3087,
"cdna_start": 1873,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1808,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000893845.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.1808G>A",
"hgvs_p": "p.Ser603Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563904.1",
"strand": false,
"transcript": "ENST00000893845.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 760,
"aa_ref": "S",
"aa_start": 603,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3130,
"cdna_start": 1890,
"cds_end": null,
"cds_length": 2283,
"cds_start": 1808,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000893846.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.1808G>A",
"hgvs_p": "p.Ser603Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000563905.1",
"strand": false,
"transcript": "ENST00000893846.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 932,
"aa_ref": "S",
"aa_start": 775,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5856,
"cdna_start": 4654,
"cds_end": null,
"cds_length": 2799,
"cds_start": 2324,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047415644.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.2324G>A",
"hgvs_p": "p.Ser775Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271600.1",
"strand": false,
"transcript": "XM_047415644.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 812,
"aa_ref": "S",
"aa_start": 655,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5496,
"cdna_start": 4294,
"cds_end": null,
"cds_length": 2439,
"cds_start": 1964,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047415645.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.1964G>A",
"hgvs_p": "p.Ser655Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271601.1",
"strand": false,
"transcript": "XM_047415645.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 644,
"aa_ref": "S",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2935,
"cdna_start": 1733,
"cds_end": null,
"cds_length": 1935,
"cds_start": 1460,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_047415646.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.1460G>A",
"hgvs_p": "p.Ser487Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271602.1",
"strand": false,
"transcript": "XM_047415646.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 644,
"aa_ref": "S",
"aa_start": 487,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6495,
"cdna_start": 5293,
"cds_end": null,
"cds_length": 1935,
"cds_start": 1460,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047415647.1",
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"hgvs_c": "c.1460G>A",
"hgvs_p": "p.Ser487Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047271603.1",
"strand": false,
"transcript": "XM_047415647.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201338298",
"effect": "missense_variant",
"frequency_reference_population": 0.000232946,
"gene_hgnc_id": 34299,
"gene_symbol": "LRRC66",
"gnomad_exomes_ac": 350,
"gnomad_exomes_af": 0.000239419,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 26,
"gnomad_genomes_af": 0.00017079,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not specified|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.13,
"pos": 51994854,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.008,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001024611.3"
}
]
}