rs9331939
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001831.4(CLU):c.984C>T(p.Asp328=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00971 in 1,614,184 control chromosomes in the GnomAD database, including 112 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0061 ( 4 hom., cov: 32)
Exomes 𝑓: 0.010 ( 108 hom. )
Consequence
CLU
NM_001831.4 synonymous
NM_001831.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.204
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
?
Variant 8-27599960-G-A is Benign according to our data. Variant chr8-27599960-G-A is described in ClinVar as [Benign]. Clinvar id is 788866.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.204 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00607 (924/152312) while in subpopulation SAS AF= 0.0228 (110/4826). AF 95% confidence interval is 0.0193. There are 4 homozygotes in gnomad4. There are 459 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 924 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLU | NM_001831.4 | c.984C>T | p.Asp328= | synonymous_variant | 7/9 | ENST00000316403.15 | |
CLU | NR_038335.2 | n.1239C>T | non_coding_transcript_exon_variant | 7/9 | |||
CLU | NR_045494.1 | n.1164C>T | non_coding_transcript_exon_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLU | ENST00000316403.15 | c.984C>T | p.Asp328= | synonymous_variant | 7/9 | 1 | NM_001831.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00607 AC: 924AN: 152194Hom.: 4 Cov.: 32
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GnomAD3 exomes AF: 0.00901 AC: 2264AN: 251386Hom.: 21 AF XY: 0.00998 AC XY: 1356AN XY: 135892
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GnomAD4 exome AF: 0.0101 AC: 14748AN: 1461872Hom.: 108 Cov.: 31 AF XY: 0.0105 AC XY: 7604AN XY: 727240
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GnomAD4 genome ? AF: 0.00607 AC: 924AN: 152312Hom.: 4 Cov.: 32 AF XY: 0.00616 AC XY: 459AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at