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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: 5-110756711-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=110756711&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 17,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "SLC25A46",
"hgnc_id": 25198,
"hgvs_c": "c.630C>T",
"hgvs_p": "p.Tyr210Tyr",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -17,
"transcript": "NM_138773.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1",
"acmg_score": -17,
"allele_count_reference_population": 224,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"chr": "5",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " hereditary motor and sensory, type 6B,Inborn genetic diseases,Neuropathy",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.5400000214576721,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 418,
"aa_ref": "Y",
"aa_start": 210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4745,
"cdna_start": 743,
"cds_end": null,
"cds_length": 1257,
"cds_start": 630,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_138773.4",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.630C>T",
"hgvs_p": "p.Tyr210Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000355943.8",
"protein_coding": true,
"protein_id": "NP_620128.1",
"strand": true,
"transcript": "NM_138773.4",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 418,
"aa_ref": "Y",
"aa_start": 210,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4745,
"cdna_start": 743,
"cds_end": null,
"cds_length": 1257,
"cds_start": 630,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000355943.8",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.630C>T",
"hgvs_p": "p.Tyr210Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138773.4",
"protein_coding": true,
"protein_id": "ENSP00000348211.3",
"strand": true,
"transcript": "ENST00000355943.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 205,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1596,
"cdna_start": null,
"cds_end": null,
"cds_length": 618,
"cds_start": null,
"consequences": [
"5_prime_UTR_premature_start_codon_gain_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000509432.1",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000426604.1",
"strand": true,
"transcript": "ENST00000509432.1",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 416,
"aa_ref": "Y",
"aa_start": 210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2661,
"cdna_start": 733,
"cds_end": null,
"cds_length": 1251,
"cds_start": 630,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000923605.1",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.630C>T",
"hgvs_p": "p.Tyr210Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000593664.1",
"strand": true,
"transcript": "ENST00000923605.1",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 337,
"aa_ref": "Y",
"aa_start": 210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4502,
"cdna_start": 743,
"cds_end": null,
"cds_length": 1014,
"cds_start": 630,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001303249.3",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.630C>T",
"hgvs_p": "p.Tyr210Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001290178.1",
"strand": true,
"transcript": "NM_001303249.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 337,
"aa_ref": "Y",
"aa_start": 210,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1575,
"cdna_start": 709,
"cds_end": null,
"cds_length": 1014,
"cds_start": 630,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000447245.6",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.630C>T",
"hgvs_p": "p.Tyr210Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000399717.2",
"strand": true,
"transcript": "ENST00000447245.6",
"transcript_support_level": 2
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 327,
"aa_ref": "Y",
"aa_start": 119,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4452,
"cdna_start": 450,
"cds_end": null,
"cds_length": 984,
"cds_start": 357,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001303250.3",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.357C>T",
"hgvs_p": "p.Tyr119Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001290179.1",
"strand": true,
"transcript": "NM_001303250.3",
"transcript_support_level": null
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 272,
"aa_ref": "Y",
"aa_start": 64,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2345,
"cdna_start": 716,
"cds_end": null,
"cds_length": 819,
"cds_start": 192,
"consequences": [
"synonymous_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000504098.1",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.192C>T",
"hgvs_p": "p.Tyr64Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000425708.1",
"strand": true,
"transcript": "ENST00000504098.1",
"transcript_support_level": 5
},
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 256,
"aa_ref": "Y",
"aa_start": 48,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1546,
"cdna_start": 434,
"cds_end": null,
"cds_length": 771,
"cds_start": 144,
"consequences": [
"synonymous_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000513807.5",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.144C>T",
"hgvs_p": "p.Tyr48Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000421134.1",
"strand": true,
"transcript": "ENST00000513807.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 205,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1596,
"cdna_start": null,
"cds_end": null,
"cds_length": 618,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000509432.1",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "c.-10C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000426604.1",
"strand": true,
"transcript": "ENST00000509432.1",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1446,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000502462.6",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "n.946C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000502462.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 558,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000508781.5",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "n.459C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000508781.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 6236,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000513706.2",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "n.2230C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000513706.2",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4871,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NR_138151.2",
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"hgvs_c": "n.869C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_138151.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201039547",
"effect": "synonymous_variant",
"frequency_reference_population": 0.00014245612,
"gene_hgnc_id": 25198,
"gene_symbol": "SLC25A46",
"gnomad_exomes_ac": 193,
"gnomad_exomes_af": 0.000135876,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 31,
"gnomad_genomes_af": 0.000203947,
"gnomad_genomes_homalt": 1,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "Neuropathy, hereditary motor and sensory, type 6B|Inborn genetic diseases",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.299,
"pos": 110756711,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_138773.4"
}
]
}