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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: 2-48725689-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=48725689&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 48725689,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000294954.12",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Arg124*",
"transcript": "NM_000233.4",
"protein_id": "NP_000224.2",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 699,
"cds_start": 370,
"cds_end": null,
"cds_length": 2100,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 3076,
"mane_select": "ENST00000294954.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Arg124*",
"transcript": "ENST00000294954.12",
"protein_id": "ENSP00000294954.6",
"transcript_support_level": 1,
"aa_start": 124,
"aa_end": null,
"aa_length": 699,
"cds_start": 370,
"cds_end": null,
"cds_length": 2100,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 3076,
"mane_select": "NM_000233.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000279956",
"gene_hgnc_id": null,
"hgvs_c": "n.295C>T",
"hgvs_p": null,
"transcript": "ENST00000602369.3",
"protein_id": "ENSP00000473498.1",
"transcript_support_level": 5,
"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": 2103,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Arg124*",
"transcript": "ENST00000405626.5",
"protein_id": "ENSP00000386033.1",
"transcript_support_level": 5,
"aa_start": 124,
"aa_end": null,
"aa_length": 672,
"cds_start": 370,
"cds_end": null,
"cds_length": 2019,
"cdna_start": 370,
"cdna_end": null,
"cdna_length": 2073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Arg124*",
"transcript": "ENST00000403273.5",
"protein_id": "ENSP00000385847.1",
"transcript_support_level": 5,
"aa_start": 124,
"aa_end": null,
"aa_length": 329,
"cds_start": 370,
"cds_end": null,
"cds_length": 990,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 1921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Arg124*",
"transcript": "ENST00000401907.5",
"protein_id": "ENSP00000385406.1",
"transcript_support_level": 5,
"aa_start": 124,
"aa_end": null,
"aa_length": 325,
"cds_start": 370,
"cds_end": null,
"cds_length": 978,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 1477,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.268C>T",
"hgvs_p": "p.Arg90*",
"transcript": "ENST00000428232.2",
"protein_id": "ENSP00000403748.1",
"transcript_support_level": 5,
"aa_start": 90,
"aa_end": null,
"aa_length": 175,
"cds_start": 268,
"cds_end": null,
"cds_length": 528,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 2174,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.295C>T",
"hgvs_p": "p.Arg99*",
"transcript": "XM_047444291.1",
"protein_id": "XP_047300247.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 674,
"cds_start": 295,
"cds_end": null,
"cds_length": 2025,
"cdna_start": 348,
"cdna_end": null,
"cdna_length": 3001,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Arg124*",
"transcript": "XM_047444292.1",
"protein_id": "XP_047300248.1",
"transcript_support_level": null,
"aa_start": 124,
"aa_end": null,
"aa_length": 637,
"cds_start": 370,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 2890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"hgvs_c": "c.295C>T",
"hgvs_p": "p.Arg99*",
"transcript": "XM_047444293.1",
"protein_id": "XP_047300249.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 612,
"cds_start": 295,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 348,
"cdna_end": null,
"cdna_length": 2815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.3442-50591G>A",
"hgvs_p": null,
"transcript": "NM_001198593.2",
"protein_id": "NP_001185522.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "STON1-GTF2A1L",
"gene_hgnc_id": 30651,
"hgvs_c": "c.3442-50591G>A",
"hgvs_p": null,
"transcript": "ENST00000402114.6",
"protein_id": "ENSP00000385701.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 1158,
"cds_start": -4,
"cds_end": null,
"cds_length": 3477,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "GTF2A1L",
"gene_hgnc_id": 30727,
"hgvs_c": "c.277-7204G>A",
"hgvs_p": null,
"transcript": "ENST00000508440.1",
"protein_id": "ENSP00000421474.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 102,
"cds_start": -4,
"cds_end": null,
"cds_length": 309,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "LHCGR",
"gene_hgnc_id": 6585,
"dbsnp": "rs773279269",
"frequency_reference_population": 0.0000020545779,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205458,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.2199999988079071,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.5,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.732,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.22,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000294954.12",
"gene_symbol": "LHCGR",
"hgnc_id": 6585,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.370C>T",
"hgvs_p": "p.Arg124*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000602369.3",
"gene_symbol": "ENSG00000279956",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.295C>T",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_001198593.2",
"gene_symbol": "STON1-GTF2A1L",
"hgnc_id": 30651,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.3442-50591G>A",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000508440.1",
"gene_symbol": "GTF2A1L",
"hgnc_id": 30727,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.277-7204G>A",
"hgvs_p": null
}
],
"clinvar_disease": "LHCGR-related disorder,Leydig cell agenesis,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1",
"phenotype_combined": "Leydig cell agenesis|not provided|LHCGR-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}