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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: 19-40757356-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=40757356&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 40757356,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000243563.8",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "c.98T>C",
"hgvs_p": "p.Ile33Thr",
"transcript": "NM_004596.5",
"protein_id": "NP_004587.1",
"transcript_support_level": null,
"aa_start": 33,
"aa_end": null,
"aa_length": 282,
"cds_start": 98,
"cds_end": null,
"cds_length": 849,
"cdna_start": 304,
"cdna_end": null,
"cdna_length": 1277,
"mane_select": "ENST00000243563.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "c.98T>C",
"hgvs_p": "p.Ile33Thr",
"transcript": "ENST00000243563.8",
"protein_id": "ENSP00000243563.2",
"transcript_support_level": 1,
"aa_start": 33,
"aa_end": null,
"aa_length": 282,
"cds_start": 98,
"cds_end": null,
"cds_length": 849,
"cdna_start": 304,
"cdna_end": null,
"cdna_length": 1277,
"mane_select": "NM_004596.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "c.98T>C",
"hgvs_p": "p.Ile33Thr",
"transcript": "ENST00000601393.1",
"protein_id": "ENSP00000472355.1",
"transcript_support_level": 3,
"aa_start": 33,
"aa_end": null,
"aa_length": 255,
"cds_start": 98,
"cds_end": null,
"cds_length": 769,
"cdna_start": 298,
"cdna_end": null,
"cdna_length": 969,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"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": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "c.98T>C",
"hgvs_p": "p.Ile33Thr",
"transcript": "ENST00000597353.5",
"protein_id": "ENSP00000472449.1",
"transcript_support_level": 5,
"aa_start": 33,
"aa_end": null,
"aa_length": 147,
"cds_start": 98,
"cds_end": null,
"cds_length": 446,
"cdna_start": 190,
"cdna_end": null,
"cdna_length": 538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "c.98T>C",
"hgvs_p": "p.Ile33Thr",
"transcript": "ENST00000599362.5",
"protein_id": "ENSP00000472258.1",
"transcript_support_level": 2,
"aa_start": 33,
"aa_end": null,
"aa_length": 141,
"cds_start": 98,
"cds_end": null,
"cds_length": 426,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 555,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "c.98T>C",
"hgvs_p": "p.Ile33Thr",
"transcript": "ENST00000601253.5",
"protein_id": "ENSP00000469224.1",
"transcript_support_level": 3,
"aa_start": 33,
"aa_end": null,
"aa_length": 127,
"cds_start": 98,
"cds_end": null,
"cds_length": 386,
"cdna_start": 231,
"cdna_end": null,
"cdna_length": 519,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "n.321T>C",
"hgvs_p": null,
"transcript": "ENST00000598452.1",
"protein_id": null,
"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": 679,
"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": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "n.233T>C",
"hgvs_p": null,
"transcript": "ENST00000598923.1",
"protein_id": null,
"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": 952,
"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": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "n.98T>C",
"hgvs_p": null,
"transcript": "ENST00000600456.1",
"protein_id": "ENSP00000471230.1",
"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": 592,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "c.-53T>C",
"hgvs_p": null,
"transcript": "ENST00000601545.5",
"protein_id": "ENSP00000470534.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 183,
"cds_start": -4,
"cds_end": null,
"cds_length": 553,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 695,
"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": "SNRPA",
"gene_hgnc_id": 11151,
"hgvs_c": "n.608-11T>C",
"hgvs_p": null,
"transcript": "ENST00000599570.5",
"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": 925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SNRPA",
"gene_hgnc_id": 11151,
"dbsnp": "rs1555775208",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7721076607704163,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.499,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9991,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.824,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3,PP5_Moderate",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000243563.8",
"gene_symbol": "SNRPA",
"hgnc_id": 11151,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.98T>C",
"hgvs_p": "p.Ile33Thr"
}
],
"clinvar_disease": "Spliceosomepathy",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Spliceosomepathy",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}