rs3087554
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001831.4(CLU):c.*316A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 594,824 control chromosomes in the GnomAD database, including 13,937 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 0.21 ( 3417 hom., cov: 31)
Exomes 𝑓: 0.21 ( 10520 hom. )
Consequence
CLU
NM_001831.4 3_prime_UTR
NM_001831.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.94
Genes affected
CLU (HGNC:2095): (clusterin) The protein encoded by this gene is a secreted chaperone that can under some stress conditions also be found in the cell cytosol. It has been suggested to be involved in several basic biological events such as cell death, tumor progression, and neurodegenerative disorders. Alternate splicing results in both coding and non-coding variants.[provided by RefSeq, May 2011]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLU | NM_001831.4 | c.*316A>G | 3_prime_UTR_variant | 9/9 | ENST00000316403.15 | ||
CLU | NR_038335.2 | n.1921A>G | non_coding_transcript_exon_variant | 9/9 | |||
CLU | NR_045494.1 | n.1846A>G | non_coding_transcript_exon_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLU | ENST00000316403.15 | c.*316A>G | 3_prime_UTR_variant | 9/9 | 1 | NM_001831.4 | P1 | ||
CLU | ENST00000405140.7 | c.*316A>G | 3_prime_UTR_variant | 9/9 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.207 AC: 31350AN: 151802Hom.: 3414 Cov.: 31
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GnomAD3 exomes AF: 0.230 AC: 30069AN: 130956Hom.: 3840 AF XY: 0.225 AC XY: 16103AN XY: 71468
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GnomAD4 exome AF: 0.207 AC: 91699AN: 442904Hom.: 10520 Cov.: 0 AF XY: 0.210 AC XY: 51257AN XY: 243780
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GnomAD4 genome ? AF: 0.207 AC: 31373AN: 151920Hom.: 3417 Cov.: 31 AF XY: 0.211 AC XY: 15633AN XY: 74258
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ClinVar
Not reported inComputational scores
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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