rs5875
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000308059.11(DLEC1):c.*471T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 786,758 control chromosomes in the GnomAD database, including 5,865 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.14 ( 1592 hom., cov: 33)
Exomes 𝑓: 0.11 ( 4273 hom. )
Consequence
DLEC1
ENST00000308059.11 3_prime_UTR
ENST00000308059.11 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.591
Genes affected
ACAA1 (HGNC:82): (acetyl-CoA acyltransferase 1) This gene encodes an enzyme operative in the beta-oxidation system of the peroxisomes. Deficiency of this enzyme leads to pseudo-Zellweger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
DLEC1 (HGNC:2899): (DLEC1 cilia and flagella associated protein) The cytogenetic location of this gene is 3p21.3, and it is located in a region that is commonly deleted in a variety of malignancies. Down-regulation of this gene has been observed in several human cancers including lung, esophageal, renal tumors, and head and neck squamous cell carcinoma. In some cases, reduced expression of this gene in tumor cells is a result of aberrant promoter methylation. Several alternatively spliced transcripts have been observed that contain disrupted coding regions and likely encode nonfunctional proteins.[provided by RefSeq, Mar 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ACAA1 | NM_001607.4 | c.*164A>T | 3_prime_UTR_variant | 12/12 | ENST00000333167.13 | NP_001598.1 | ||
DLEC1 | NM_007335.4 | c.*471T>A | 3_prime_UTR_variant | 37/37 | ENST00000308059.11 | NP_031361.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DLEC1 | ENST00000308059.11 | c.*471T>A | 3_prime_UTR_variant | 37/37 | 1 | NM_007335.4 | ENSP00000308597 | P2 | ||
ACAA1 | ENST00000333167.13 | c.*164A>T | 3_prime_UTR_variant | 12/12 | 1 | NM_001607.4 | ENSP00000333664 | P1 |
Frequencies
GnomAD3 genomes AF: 0.137 AC: 20826AN: 151876Hom.: 1588 Cov.: 33
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GnomAD4 exome AF: 0.110 AC: 70012AN: 634764Hom.: 4273 Cov.: 8 AF XY: 0.110 AC XY: 35933AN XY: 328106
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GnomAD4 genome AF: 0.137 AC: 20847AN: 151994Hom.: 1592 Cov.: 33 AF XY: 0.137 AC XY: 10201AN XY: 74326
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at