rs10567
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_014881.5(DCLRE1A):c.*186G>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 0.0189 in 577,882 control chromosomes in the GnomAD database, including 139 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 0.016 ( 37 hom., cov: 32)
Exomes 𝑓: 0.020 ( 102 hom. )
Consequence
DCLRE1A
NM_014881.5 3_prime_UTR
NM_014881.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.04
Genes affected
DCLRE1A (HGNC:17660): (DNA cross-link repair 1A) This gene encodes a conserved protein that is involved in the repair of DNA interstrand cross-links. DNA cross-links suppress transcription, replication, and DNA segregation. The encoded protein is a regulator of the mitotic cell cycle checkpoint. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
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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=-0.87).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0163 (2475/152278) while in subpopulation NFE AF= 0.0235 (1601/68022). AF 95% confidence interval is 0.0226. There are 37 homozygotes in gnomad4. There are 1122 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 37 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCLRE1A | NM_014881.5 | c.*186G>A | 3_prime_UTR_variant | 9/9 | ENST00000361384.7 | ||
DCLRE1A | NM_001271816.2 | c.*186G>A | 3_prime_UTR_variant | 10/10 | |||
DCLRE1A | XM_006718090.2 | c.*186G>A | 3_prime_UTR_variant | 10/10 | |||
DCLRE1A | XM_011540429.2 | c.*186G>A | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCLRE1A | ENST00000361384.7 | c.*186G>A | 3_prime_UTR_variant | 9/9 | 1 | NM_014881.5 | P1 | ||
DCLRE1A | ENST00000369305.1 | c.*186G>A | 3_prime_UTR_variant | 10/10 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0163 AC: 2479AN: 152160Hom.: 37 Cov.: 32
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GnomAD4 exome AF: 0.0198 AC: 8426AN: 425604Hom.: 102 Cov.: 6 AF XY: 0.0192 AC XY: 4259AN XY: 221876
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at