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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: 4-15596207-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=15596207&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 15596207,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_001080522.2",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4437G>A",
"hgvs_p": "p.Gln1479Gln",
"transcript": "NM_001378615.1",
"protein_id": "NP_001365544.1",
"transcript_support_level": null,
"aa_start": 1479,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4437,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 4631,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "ENST00000424120.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378615.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4437G>A",
"hgvs_p": "p.Gln1479Gln",
"transcript": "ENST00000424120.6",
"protein_id": "ENSP00000403465.1",
"transcript_support_level": 5,
"aa_start": 1479,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4437,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 4631,
"cdna_end": null,
"cdna_length": 5184,
"mane_select": "NM_001378615.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000424120.6"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4437G>A",
"hgvs_p": "p.Gln1479Gln",
"transcript": "ENST00000503292.6",
"protein_id": "ENSP00000421809.1",
"transcript_support_level": 1,
"aa_start": 1479,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4437,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 4676,
"cdna_end": null,
"cdna_length": 5226,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000503292.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.4231G>A",
"hgvs_p": null,
"transcript": "ENST00000634028.2",
"protein_id": "ENSP00000488669.2",
"transcript_support_level": 1,
"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": 4784,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000634028.2"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4473G>A",
"hgvs_p": "p.Gln1491Gln",
"transcript": "ENST00000389652.11",
"protein_id": "ENSP00000374303.8",
"transcript_support_level": 5,
"aa_start": 1491,
"aa_end": null,
"aa_length": 1632,
"cds_start": 4473,
"cds_end": null,
"cds_length": 4899,
"cdna_start": 4491,
"cdna_end": null,
"cdna_length": 5044,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000389652.11"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4458G>A",
"hgvs_p": "p.Gln1486Gln",
"transcript": "ENST00000951218.1",
"protein_id": "ENSP00000621277.1",
"transcript_support_level": null,
"aa_start": 1486,
"aa_end": null,
"aa_length": 1627,
"cds_start": 4458,
"cds_end": null,
"cds_length": 4884,
"cdna_start": 4647,
"cdna_end": null,
"cdna_length": 5193,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951218.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 35,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4437G>A",
"hgvs_p": "p.Gln1479Gln",
"transcript": "NM_001080522.2",
"protein_id": "NP_001073991.2",
"transcript_support_level": null,
"aa_start": 1479,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4437,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 4682,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001080522.2"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4437G>A",
"hgvs_p": "p.Gln1479Gln",
"transcript": "ENST00000860661.1",
"protein_id": "ENSP00000530720.1",
"transcript_support_level": null,
"aa_start": 1479,
"aa_end": null,
"aa_length": 1620,
"cds_start": 4437,
"cds_end": null,
"cds_length": 4863,
"cdna_start": 4608,
"cdna_end": null,
"cdna_length": 5706,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860661.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 34,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4428G>A",
"hgvs_p": "p.Gln1476Gln",
"transcript": "ENST00000951219.1",
"protein_id": "ENSP00000621278.1",
"transcript_support_level": null,
"aa_start": 1476,
"aa_end": null,
"aa_length": 1617,
"cds_start": 4428,
"cds_end": null,
"cds_length": 4854,
"cdna_start": 4607,
"cdna_end": null,
"cdna_length": 5157,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000951219.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4296G>A",
"hgvs_p": "p.Gln1432Gln",
"transcript": "ENST00000860662.1",
"protein_id": "ENSP00000530721.1",
"transcript_support_level": null,
"aa_start": 1432,
"aa_end": null,
"aa_length": 1573,
"cds_start": 4296,
"cds_end": null,
"cds_length": 4722,
"cdna_start": 4495,
"cdna_end": null,
"cdna_length": 5042,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860662.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4290G>A",
"hgvs_p": "p.Gln1430Gln",
"transcript": "NM_001378617.1",
"protein_id": "NP_001365546.1",
"transcript_support_level": null,
"aa_start": 1430,
"aa_end": null,
"aa_length": 1571,
"cds_start": 4290,
"cds_end": null,
"cds_length": 4716,
"cdna_start": 4431,
"cdna_end": null,
"cdna_length": 4984,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378617.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 35,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4290G>A",
"hgvs_p": "p.Gln1430Gln",
"transcript": "ENST00000506643.5",
"protein_id": "ENSP00000422931.2",
"transcript_support_level": 2,
"aa_start": 1430,
"aa_end": null,
"aa_length": 1571,
"cds_start": 4290,
"cds_end": null,
"cds_length": 4716,
"cdna_start": 4439,
"cdna_end": null,
"cdna_length": 4989,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000506643.5"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.4113G>A",
"hgvs_p": "p.Gln1371Gln",
"transcript": "ENST00000674945.1",
"protein_id": "ENSP00000502333.1",
"transcript_support_level": null,
"aa_start": 1371,
"aa_end": null,
"aa_length": 1512,
"cds_start": 4113,
"cds_end": null,
"cds_length": 4539,
"cdna_start": 4262,
"cdna_end": null,
"cdna_length": 4809,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674945.1"
},
{
"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": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "c.544-1200G>A",
"hgvs_p": null,
"transcript": "ENST00000514039.6",
"protein_id": "ENSP00000488534.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 322,
"cds_start": null,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 969,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000514039.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.336G>A",
"hgvs_p": null,
"transcript": "ENST00000513035.2",
"protein_id": null,
"transcript_support_level": 2,
"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": 406,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000513035.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.*1934G>A",
"hgvs_p": null,
"transcript": "ENST00000650860.2",
"protein_id": "ENSP00000498775.1",
"transcript_support_level": null,
"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": 5513,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000650860.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.5096G>A",
"hgvs_p": null,
"transcript": "ENST00000680586.1",
"protein_id": null,
"transcript_support_level": null,
"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": 6514,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000680586.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 36,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"hgvs_c": "n.*1934G>A",
"hgvs_p": null,
"transcript": "ENST00000650860.2",
"protein_id": "ENSP00000498775.1",
"transcript_support_level": null,
"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": 5513,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000650860.2"
}
],
"gene_symbol": "CC2D2A",
"gene_hgnc_id": 29253,
"dbsnp": "rs878854168",
"frequency_reference_population": 7.3658964e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.3659e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.377,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.91,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999973119681478,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_001080522.2",
"gene_symbol": "CC2D2A",
"hgnc_id": 29253,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4437G>A",
"hgvs_p": "p.Gln1479Gln"
}
],
"clinvar_disease": "Joubert syndrome,Meckel-Gruber syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Meckel-Gruber syndrome;Joubert syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}