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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: 10-49474056-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=49474056&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 49474056,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000355832.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"transcript": "NM_000124.4",
"protein_id": "NP_000115.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 1493,
"cds_start": 2569,
"cds_end": null,
"cds_length": 4482,
"cdna_start": 2743,
"cdna_end": null,
"cdna_length": 9001,
"mane_select": "ENST00000355832.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"transcript": "ENST00000355832.10",
"protein_id": "ENSP00000348089.5",
"transcript_support_level": 1,
"aa_start": 857,
"aa_end": null,
"aa_length": 1493,
"cds_start": 2569,
"cds_end": null,
"cds_length": 4482,
"cdna_start": 2743,
"cdna_end": null,
"cdna_length": 9001,
"mane_select": "NM_000124.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "n.6953C>T",
"hgvs_p": null,
"transcript": "ENST00000623073.3",
"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": 11026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "n.*168C>T",
"hgvs_p": null,
"transcript": "ENST00000624341.3",
"protein_id": "ENSP00000485163.1",
"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": 5761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "n.*168C>T",
"hgvs_p": null,
"transcript": "ENST00000624341.3",
"protein_id": "ENSP00000485163.1",
"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": 5761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*",
"transcript": "NM_001346440.2",
"protein_id": "NP_001333369.1",
"transcript_support_level": null,
"aa_start": 857,
"aa_end": null,
"aa_length": 1493,
"cds_start": 2569,
"cds_end": null,
"cds_length": 4482,
"cdna_start": 2739,
"cdna_end": null,
"cdna_length": 28586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "c.2410C>T",
"hgvs_p": "p.Arg804*",
"transcript": "ENST00000681659.1",
"protein_id": "ENSP00000505631.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1440,
"cds_start": 2410,
"cds_end": null,
"cds_length": 4323,
"cdna_start": 2514,
"cdna_end": null,
"cdna_length": 9074,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "n.992C>T",
"hgvs_p": null,
"transcript": "ENST00000623115.3",
"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": 2932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"hgvs_c": "n.2647C>T",
"hgvs_p": null,
"transcript": "ENST00000681632.1",
"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": 10532,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ERCC6",
"gene_hgnc_id": 3438,
"dbsnp": "rs751448793",
"frequency_reference_population": 0.000017969496,
"hom_count_reference_population": 0,
"allele_count_reference_population": 29,
"gnomad_exomes_af": 0.0000184715,
"gnomad_genomes_af": 0.0000131465,
"gnomad_exomes_ac": 27,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6200000047683716,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.4399999976158142,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.651,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.44,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000355832.10",
"gene_symbol": "ERCC6",
"hgnc_id": 3438,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.2569C>T",
"hgvs_p": "p.Arg857*"
}
],
"clinvar_disease": "Cerebrooculofacioskeletal syndrome 1,Cockayne syndrome type 2,DE SANCTIS-CACCHIONE SYNDROME,ERCC6-related disorder,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:3",
"phenotype_combined": "Cockayne syndrome type 2;DE SANCTIS-CACCHIONE SYNDROME;Cerebrooculofacioskeletal syndrome 1|not provided|ERCC6-related disorder|Cockayne syndrome type 2",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}