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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: 2-96287968-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=96287968&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 96287968,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_014014.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "c.3260C>T",
"hgvs_p": "p.Ser1087Leu",
"transcript": "NM_014014.5",
"protein_id": "NP_054733.2",
"transcript_support_level": null,
"aa_start": 1087,
"aa_end": null,
"aa_length": 2136,
"cds_start": 3260,
"cds_end": null,
"cds_length": 6411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000323853.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014014.5"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "c.3260C>T",
"hgvs_p": "p.Ser1087Leu",
"transcript": "ENST00000323853.10",
"protein_id": "ENSP00000317123.5",
"transcript_support_level": 1,
"aa_start": 1087,
"aa_end": null,
"aa_length": 2136,
"cds_start": 3260,
"cds_end": null,
"cds_length": 6411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014014.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000323853.10"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "c.3293C>T",
"hgvs_p": "p.Ser1098Leu",
"transcript": "ENST00000914240.1",
"protein_id": "ENSP00000584299.1",
"transcript_support_level": null,
"aa_start": 1098,
"aa_end": null,
"aa_length": 2147,
"cds_start": 3293,
"cds_end": null,
"cds_length": 6444,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000914240.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "c.3257C>T",
"hgvs_p": "p.Ser1086Leu",
"transcript": "ENST00000960227.1",
"protein_id": "ENSP00000630286.1",
"transcript_support_level": null,
"aa_start": 1086,
"aa_end": null,
"aa_length": 2135,
"cds_start": 3257,
"cds_end": null,
"cds_length": 6408,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960227.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 45,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "c.3260C>T",
"hgvs_p": "p.Ser1087Leu",
"transcript": "ENST00000960226.1",
"protein_id": "ENSP00000630285.1",
"transcript_support_level": null,
"aa_start": 1087,
"aa_end": null,
"aa_length": 2134,
"cds_start": 3260,
"cds_end": null,
"cds_length": 6405,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000960226.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "c.3176C>T",
"hgvs_p": "p.Ser1059Leu",
"transcript": "ENST00000880043.1",
"protein_id": "ENSP00000550102.1",
"transcript_support_level": null,
"aa_start": 1059,
"aa_end": null,
"aa_length": 2108,
"cds_start": 3176,
"cds_end": null,
"cds_length": 6327,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000880043.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "c.3260C>T",
"hgvs_p": "p.Ser1087Leu",
"transcript": "ENST00000652267.1",
"protein_id": "ENSP00000498933.1",
"transcript_support_level": null,
"aa_start": 1087,
"aa_end": null,
"aa_length": 1374,
"cds_start": 3260,
"cds_end": null,
"cds_length": 4127,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000652267.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"hgvs_c": "n.377C>T",
"hgvs_p": null,
"transcript": "ENST00000480615.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000480615.1"
}
],
"gene_symbol": "SNRNP200",
"gene_hgnc_id": 30859,
"dbsnp": "rs267607077",
"frequency_reference_population": 0.0000061569194,
"hom_count_reference_population": 0,
"allele_count_reference_population": 9,
"gnomad_exomes_af": 0.00000615692,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9674351811408997,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8119999766349792,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.672,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.96,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.419,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.97692799036931,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 15,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PS3,PM1,PP3,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 15,
"benign_score": 0,
"pathogenic_score": 15,
"criteria": [
"PS3",
"PM1",
"PP3",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_014014.5",
"gene_symbol": "SNRNP200",
"hgnc_id": 30859,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3260C>T",
"hgvs_p": "p.Ser1087Leu"
}
],
"clinvar_disease": "Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 33,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 US:1",
"phenotype_combined": "Retinitis pigmentosa 33|Retinitis pigmentosa|not provided|Retinal dystrophy",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}