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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: 12-49042338-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=49042338&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 18,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"splice_region_variant",
"intron_variant"
],
"gene_symbol": "KMT2D",
"hgnc_id": 7133,
"hgvs_c": "c.5868-8C>T",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -18,
"transcript": "NM_003482.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_score": -18,
"allele_count_reference_population": 2709,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "12",
"clinvar_classification": "Benign",
"clinvar_disease": "Kabuki syndrome,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.36000001430511475,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 5537,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 20635,
"cdna_start": null,
"cds_end": null,
"cds_length": 16614,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 55,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_003482.4",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.5868-8C>T",
"hgvs_p": null,
"intron_rank": 28,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000301067.12",
"protein_coding": true,
"protein_id": "NP_003473.3",
"strand": false,
"transcript": "NM_003482.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 5537,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 20635,
"cdna_start": null,
"cds_end": null,
"cds_length": 16614,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 55,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000301067.12",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.5868-8C>T",
"hgvs_p": null,
"intron_rank": 28,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003482.4",
"protein_coding": true,
"protein_id": "ENSP00000301067.7",
"strand": false,
"transcript": "ENST00000301067.12",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 5553,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 20686,
"cdna_start": null,
"cds_end": null,
"cds_length": 16662,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 56,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000683543.2",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.5868-8C>T",
"hgvs_p": null,
"intron_rank": 28,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000506726.1",
"strand": false,
"transcript": "ENST00000683543.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 5540,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16623,
"cdna_start": null,
"cds_end": null,
"cds_length": 16623,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 54,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000685166.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.5877-8C>T",
"hgvs_p": null,
"intron_rank": 27,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509386.1",
"strand": false,
"transcript": "ENST00000685166.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 5536,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16611,
"cdna_start": null,
"cds_end": null,
"cds_length": 16611,
"cds_start": null,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_count": 54,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000692637.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.5865-8C>T",
"hgvs_p": null,
"intron_rank": 27,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509666.1",
"strand": false,
"transcript": "ENST00000692637.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 340,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1025,
"cdna_start": null,
"cds_end": null,
"cds_length": 1023,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 9,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650290.2",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.678-29C>T",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000497218.2",
"strand": false,
"transcript": "ENST00000650290.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 823,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2475,
"cdna_start": null,
"cds_end": null,
"cds_length": 2474,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000689944.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.-30C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000508812.1",
"strand": true,
"transcript": "ENST00000689944.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 793,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2385,
"cdna_start": null,
"cds_end": null,
"cds_length": 2384,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000689060.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "c.-30C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000509018.1",
"strand": true,
"transcript": "ENST00000689060.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1816,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000688095.1",
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"hgvs_c": "n.*899C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000510007.1",
"strand": true,
"transcript": "ENST00000688095.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0031548164147271,
"dbsnp": "rs75783546",
"effect": "splice_region_variant,intron_variant",
"frequency_reference_population": 0.0017838682,
"gene_hgnc_id": 7133,
"gene_symbol": "KMT2D",
"gnomad_exomes_ac": 1395,
"gnomad_exomes_af": 0.00102093,
"gnomad_exomes_homalt": 19,
"gnomad_genomes_ac": 1314,
"gnomad_genomes_af": 0.00863258,
"gnomad_genomes_homalt": 23,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 42,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Kabuki syndrome|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.192,
"pos": 49042338,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.1120000034570694,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003482.4"
}
]
}