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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: 1-244842055-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=244842055&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 244842055,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000411948.7",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "c.154A>C",
"hgvs_p": "p.Thr52Pro",
"transcript": "NM_198076.6",
"protein_id": "NP_932342.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 118,
"cds_start": 154,
"cds_end": null,
"cds_length": 357,
"cdna_start": 211,
"cdna_end": null,
"cdna_length": 2295,
"mane_select": "ENST00000411948.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "c.154A>C",
"hgvs_p": "p.Thr52Pro",
"transcript": "ENST00000411948.7",
"protein_id": "ENSP00000406327.2",
"transcript_support_level": 1,
"aa_start": 52,
"aa_end": null,
"aa_length": 118,
"cds_start": 154,
"cds_end": null,
"cds_length": 357,
"cdna_start": 211,
"cdna_end": null,
"cdna_length": 2295,
"mane_select": "NM_198076.6",
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "n.102-140A>C",
"hgvs_p": null,
"transcript": "ENST00000391839.6",
"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": 1005,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "c.190A>C",
"hgvs_p": "p.Thr64Pro",
"transcript": "NM_001312872.1",
"protein_id": "NP_001299801.1",
"transcript_support_level": null,
"aa_start": 64,
"aa_end": null,
"aa_length": 130,
"cds_start": 190,
"cds_end": null,
"cds_length": 393,
"cdna_start": 429,
"cdna_end": null,
"cdna_length": 2519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "c.190A>C",
"hgvs_p": "p.Thr64Pro",
"transcript": "ENST00000366528.3",
"protein_id": "ENSP00000355486.3",
"transcript_support_level": 2,
"aa_start": 64,
"aa_end": null,
"aa_length": 130,
"cds_start": 190,
"cds_end": null,
"cds_length": 393,
"cdna_start": 289,
"cdna_end": null,
"cdna_length": 568,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "c.154A>C",
"hgvs_p": "p.Thr52Pro",
"transcript": "NM_001312871.1",
"protein_id": "NP_001299800.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 118,
"cds_start": 154,
"cds_end": null,
"cds_length": 357,
"cdna_start": 421,
"cdna_end": null,
"cdna_length": 2511,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "c.154A>C",
"hgvs_p": "p.Thr52Pro",
"transcript": "NM_001312874.1",
"protein_id": "NP_001299803.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 61,
"cds_start": 154,
"cds_end": null,
"cds_length": 186,
"cdna_start": 393,
"cdna_end": null,
"cdna_length": 2479,
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HNRNPU",
"gene_hgnc_id": 5048,
"hgvs_c": "n.11435T>G",
"hgvs_p": null,
"transcript": "ENST00000366527.4",
"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": 12852,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "n.2309A>C",
"hgvs_p": null,
"transcript": "ENST00000464757.1",
"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": 2616,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HNRNPU",
"gene_hgnc_id": 5048,
"hgvs_c": "n.*3414T>G",
"hgvs_p": null,
"transcript": "ENST00000475997.6",
"protein_id": "ENSP00000482621.2",
"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": 5290,
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "n.210A>C",
"hgvs_p": null,
"transcript": "ENST00000498262.1",
"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": 2290,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HNRNPU",
"gene_hgnc_id": 5048,
"hgvs_c": "n.11716T>G",
"hgvs_p": null,
"transcript": "ENST00000649899.1",
"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": 13084,
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "n.373A>C",
"hgvs_p": null,
"transcript": "NR_132420.1",
"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": 2463,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HNRNPU",
"gene_hgnc_id": 5048,
"hgvs_c": "n.*3414T>G",
"hgvs_p": null,
"transcript": "ENST00000475997.6",
"protein_id": "ENSP00000482621.2",
"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": 5290,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "c.23-140A>C",
"hgvs_p": null,
"transcript": "NM_001312873.1",
"protein_id": "NP_001299802.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 73,
"cds_start": -4,
"cds_end": null,
"cds_length": 222,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2348,
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "n.282-140A>C",
"hgvs_p": null,
"transcript": "NR_132419.1",
"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": 2368,
"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": "COX20",
"gene_hgnc_id": 26970,
"hgvs_c": "n.262-144A>C",
"hgvs_p": null,
"transcript": "NR_132421.1",
"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": 2344,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COX20",
"gene_hgnc_id": 26970,
"dbsnp": "rs587777004",
"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": 0.9276448488235474,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.665,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.42,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.462,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.06,
"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_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000411948.7",
"gene_symbol": "COX20",
"hgnc_id": 26970,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.154A>C",
"hgvs_p": "p.Thr52Pro"
},
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000366527.4",
"gene_symbol": "HNRNPU",
"hgnc_id": 5048,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.11435T>G",
"hgvs_p": null
}
],
"clinvar_disease": " nuclear type 11,Mitochondrial complex IV deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Mitochondrial complex IV deficiency, nuclear type 11",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}