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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: X-108677633-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=108677633&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 108677633,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "ENST00000328300.11",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3942G>A",
"hgvs_p": "p.Gln1314Gln",
"transcript": "NM_033380.3",
"protein_id": "NP_203699.1",
"transcript_support_level": null,
"aa_start": 1314,
"aa_end": null,
"aa_length": 1691,
"cds_start": 3942,
"cds_end": null,
"cds_length": 5076,
"cdna_start": 4230,
"cdna_end": null,
"cdna_length": 6531,
"mane_select": "ENST00000328300.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3942G>A",
"hgvs_p": "p.Gln1314Gln",
"transcript": "ENST00000328300.11",
"protein_id": "ENSP00000331902.7",
"transcript_support_level": 1,
"aa_start": 1314,
"aa_end": null,
"aa_length": 1691,
"cds_start": 3942,
"cds_end": null,
"cds_length": 5076,
"cdna_start": 4230,
"cdna_end": null,
"cdna_length": 6531,
"mane_select": "NM_033380.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3924G>A",
"hgvs_p": "p.Gln1308Gln",
"transcript": "NM_000495.5",
"protein_id": "NP_000486.1",
"transcript_support_level": null,
"aa_start": 1308,
"aa_end": null,
"aa_length": 1685,
"cds_start": 3924,
"cds_end": null,
"cds_length": 5058,
"cdna_start": 4212,
"cdna_end": null,
"cdna_length": 6513,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 42,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3924G>A",
"hgvs_p": "p.Gln1308Gln",
"transcript": "ENST00000361603.7",
"protein_id": "ENSP00000354505.2",
"transcript_support_level": 2,
"aa_start": 1308,
"aa_end": null,
"aa_length": 1685,
"cds_start": 3924,
"cds_end": null,
"cds_length": 5058,
"cdna_start": 4126,
"cdna_end": null,
"cdna_length": 6427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3957G>A",
"hgvs_p": "p.Gln1319Gln",
"transcript": "XM_011530849.3",
"protein_id": "XP_011529151.2",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1696,
"cds_start": 3957,
"cds_end": null,
"cds_length": 5091,
"cdna_start": 3972,
"cdna_end": null,
"cdna_length": 6273,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 44,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3948G>A",
"hgvs_p": "p.Gln1316Gln",
"transcript": "XM_017029259.3",
"protein_id": "XP_016884748.1",
"transcript_support_level": null,
"aa_start": 1316,
"aa_end": null,
"aa_length": 1693,
"cds_start": 3948,
"cds_end": null,
"cds_length": 5082,
"cdna_start": 3963,
"cdna_end": null,
"cdna_length": 6264,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 43,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3939G>A",
"hgvs_p": "p.Gln1313Gln",
"transcript": "XM_017029260.2",
"protein_id": "XP_016884749.1",
"transcript_support_level": null,
"aa_start": 1313,
"aa_end": null,
"aa_length": 1690,
"cds_start": 3939,
"cds_end": null,
"cds_length": 5073,
"cdna_start": 3954,
"cdna_end": null,
"cdna_length": 6255,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 54,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3618G>A",
"hgvs_p": "p.Gln1206Gln",
"transcript": "XM_047441810.1",
"protein_id": "XP_047297766.1",
"transcript_support_level": null,
"aa_start": 1206,
"aa_end": null,
"aa_length": 1583,
"cds_start": 3618,
"cds_end": null,
"cds_length": 4752,
"cdna_start": 4282,
"cdna_end": null,
"cdna_length": 6583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 45,
"exon_rank_end": null,
"exon_count": 46,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "c.3957G>A",
"hgvs_p": "p.Gln1319Gln",
"transcript": "XM_017029261.2",
"protein_id": "XP_016884750.1",
"transcript_support_level": null,
"aa_start": 1319,
"aa_end": null,
"aa_length": 1330,
"cds_start": 3957,
"cds_end": null,
"cds_length": 3993,
"cdna_start": 3972,
"cdna_end": null,
"cdna_length": 4398,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "n.345G>A",
"hgvs_p": null,
"transcript": "ENST00000489230.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 737,
"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": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"hgvs_c": "n.436G>A",
"hgvs_p": null,
"transcript": "ENST00000510690.2",
"protein_id": null,
"transcript_support_level": 4,
"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": 1581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A5",
"gene_hgnc_id": 2207,
"dbsnp": "rs281874724",
"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": -0.33000001311302185,
"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": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.263,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.66,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999791011073036,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000328300.11",
"gene_symbol": "COL4A5",
"hgnc_id": 2207,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.3942G>A",
"hgvs_p": "p.Gln1314Gln"
}
],
"clinvar_disease": "X-linked Alport syndrome,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided|X-linked Alport syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}