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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: 3-40044269-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=40044269&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 40044269,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_015460.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Gln",
"transcript": "ENST00000396217.7",
"protein_id": "ENSP00000379519.3",
"transcript_support_level": 1,
"aa_start": 67,
"aa_end": null,
"aa_length": 770,
"cds_start": 200,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 617,
"cdna_end": null,
"cdna_length": 4877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala",
"transcript": "NM_015460.4",
"protein_id": "NP_056275.2",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 859,
"cds_start": 330,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 668,
"cdna_end": null,
"cdna_length": 5073,
"mane_select": "ENST00000302541.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala",
"transcript": "ENST00000302541.11",
"protein_id": "ENSP00000301972.6",
"transcript_support_level": 1,
"aa_start": 110,
"aa_end": null,
"aa_length": 859,
"cds_start": 330,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 668,
"cdna_end": null,
"cdna_length": 5073,
"mane_select": "NM_015460.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala",
"transcript": "ENST00000444716.5",
"protein_id": "ENSP00000398665.1",
"transcript_support_level": 1,
"aa_start": 110,
"aa_end": null,
"aa_length": 859,
"cds_start": 330,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 428,
"cdna_end": null,
"cdna_length": 2678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "n.330G>A",
"hgvs_p": null,
"transcript": "ENST00000458292.5",
"protein_id": "ENSP00000413392.1",
"transcript_support_level": 1,
"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": 3244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "n.330G>A",
"hgvs_p": null,
"transcript": "ENST00000458441.5",
"protein_id": "ENSP00000400916.1",
"transcript_support_level": 1,
"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": 3144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "n.589G>A",
"hgvs_p": null,
"transcript": "ENST00000475082.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 961,
"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",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.200G>A",
"hgvs_p": "p.Arg67Gln",
"transcript": "NM_001284425.2",
"protein_id": "NP_001271354.1",
"transcript_support_level": null,
"aa_start": 67,
"aa_end": null,
"aa_length": 770,
"cds_start": 200,
"cds_end": null,
"cds_length": 2313,
"cdna_start": 668,
"cdna_end": null,
"cdna_length": 4936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala",
"transcript": "NM_001284423.2",
"protein_id": "NP_001271352.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 859,
"cds_start": 330,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 428,
"cdna_end": null,
"cdna_length": 4833,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala",
"transcript": "NM_001284424.2",
"protein_id": "NP_001271353.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 794,
"cds_start": 330,
"cds_end": null,
"cds_length": 2385,
"cdna_start": 668,
"cdna_end": null,
"cdna_length": 4878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala",
"transcript": "ENST00000425621.5",
"protein_id": "ENSP00000389323.1",
"transcript_support_level": 2,
"aa_start": 110,
"aa_end": null,
"aa_length": 794,
"cds_start": 330,
"cds_end": null,
"cds_length": 2385,
"cdna_start": 571,
"cdna_end": null,
"cdna_length": 2981,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala",
"transcript": "XM_011533575.2",
"protein_id": "XP_011531877.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 859,
"cds_start": 330,
"cds_end": null,
"cds_length": 2580,
"cdna_start": 1131,
"cdna_end": null,
"cdna_length": 5536,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"hgvs_c": "n.668G>A",
"hgvs_p": null,
"transcript": "NR_104316.2",
"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": 5036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MYRIP",
"gene_hgnc_id": 19156,
"dbsnp": "rs56248790",
"frequency_reference_population": 0.0023853928,
"hom_count_reference_population": 9,
"allele_count_reference_population": 3850,
"gnomad_exomes_af": 0.00245816,
"gnomad_genomes_af": 0.00168715,
"gnomad_exomes_ac": 3593,
"gnomad_genomes_ac": 257,
"gnomad_exomes_homalt": 9,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.006328970193862915,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.057999998331069946,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.034,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.022,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.00000166858399951087,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_015460.4",
"gene_symbol": "MYRIP",
"hgnc_id": 19156,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.330G>A",
"hgvs_p": "p.Ala110Ala"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}