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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: X-124365787-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=124365787&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 124365787,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000371139.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"transcript": "NM_002351.5",
"protein_id": "NP_002342.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 128,
"cds_start": 164,
"cds_end": null,
"cds_length": 387,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 2236,
"mane_select": "ENST00000371139.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"transcript": "ENST00000371139.9",
"protein_id": "ENSP00000360181.5",
"transcript_support_level": 1,
"aa_start": 55,
"aa_end": null,
"aa_length": 128,
"cds_start": 164,
"cds_end": null,
"cds_length": 387,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 2236,
"mane_select": "NM_002351.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"transcript": "ENST00000360027.5",
"protein_id": "ENSP00000353126.4",
"transcript_support_level": 1,
"aa_start": 55,
"aa_end": null,
"aa_length": 125,
"cds_start": 164,
"cds_end": null,
"cds_length": 378,
"cdna_start": 391,
"cdna_end": null,
"cdna_length": 2059,
"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": 1,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.138-4444G>A",
"hgvs_p": null,
"transcript": "ENST00000494073.5",
"protein_id": "ENSP00000513589.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 62,
"cds_start": -4,
"cds_end": null,
"cds_length": 189,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"transcript": "ENST00000698113.1",
"protein_id": "ENSP00000513571.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 128,
"cds_start": 164,
"cds_end": null,
"cds_length": 387,
"cdna_start": 1852,
"cdna_end": null,
"cdna_length": 3840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"transcript": "ENST00000698116.1",
"protein_id": "ENSP00000513572.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 128,
"cds_start": 164,
"cds_end": null,
"cds_length": 387,
"cdna_start": 293,
"cdna_end": null,
"cdna_length": 2276,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"transcript": "ENST00000698118.1",
"protein_id": "ENSP00000513574.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 128,
"cds_start": 164,
"cds_end": null,
"cds_length": 387,
"cdna_start": 199,
"cdna_end": null,
"cdna_length": 1163,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln",
"transcript": "NM_001114937.3",
"protein_id": "NP_001108409.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 125,
"cds_start": 164,
"cds_end": null,
"cds_length": 378,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 2227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "c.142G>A",
"hgvs_p": "p.Glu48Lys",
"transcript": "ENST00000477673.2",
"protein_id": "ENSP00000477094.1",
"transcript_support_level": 2,
"aa_start": 48,
"aa_end": null,
"aa_length": 76,
"cds_start": 142,
"cds_end": null,
"cds_length": 231,
"cdna_start": 196,
"cdna_end": null,
"cdna_length": 461,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.525G>A",
"hgvs_p": null,
"transcript": "ENST00000635645.1",
"protein_id": null,
"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": 2554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.164G>A",
"hgvs_p": null,
"transcript": "ENST00000647259.2",
"protein_id": "ENSP00000494582.1",
"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": 2471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.525G>A",
"hgvs_p": null,
"transcript": "ENST00000698112.1",
"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": 2147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.99G>A",
"hgvs_p": null,
"transcript": "ENST00000698115.1",
"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": 2083,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.164G>A",
"hgvs_p": null,
"transcript": "ENST00000698117.1",
"protein_id": "ENSP00000513573.1",
"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": 2202,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.463G>A",
"hgvs_p": null,
"transcript": "ENST00000698119.1",
"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": 2446,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "STAG2",
"gene_hgnc_id": 11355,
"hgvs_c": "n.454-46035G>A",
"hgvs_p": null,
"transcript": "ENST00000469481.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 989,
"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": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.138-4389G>A",
"hgvs_p": null,
"transcript": "ENST00000491950.5",
"protein_id": "ENSP00000513588.1",
"transcript_support_level": 2,
"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": 474,
"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": "SH2D1A",
"gene_hgnc_id": 10820,
"hgvs_c": "n.117-4444G>A",
"hgvs_p": null,
"transcript": "ENST00000698114.1",
"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": 1017,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SH2D1A",
"gene_hgnc_id": 10820,
"dbsnp": "rs111033630",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9029842615127563,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.14000000059604645,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.869,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9225,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.738,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.14,
"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": 9,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 9,
"benign_score": 0,
"pathogenic_score": 9,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP3_Moderate",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000371139.9",
"gene_symbol": "SH2D1A",
"hgnc_id": 10820,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.164G>A",
"hgvs_p": "p.Arg55Gln"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000469481.1",
"gene_symbol": "STAG2",
"hgnc_id": 11355,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "n.454-46035G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Lymphoproliferative disorder,X-linked lymphoproliferative disease due to SH2D1A deficiency,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:2 US:1",
"phenotype_combined": "not provided|X-linked lymphoproliferative disease due to SH2D1A deficiency|Lymphoproliferative disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}