chr8-27605048-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_001831.4(CLU):c.705C>T(p.Tyr235=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,613,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000039 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000026 ( 0 hom. )
Consequence
CLU
NM_001831.4 synonymous
NM_001831.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.53
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 -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
?
Variant 8-27605048-G-A is Benign according to our data. Variant chr8-27605048-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 799508.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-2.53 with no splicing effect.
BS2
?
High AC in GnomAd at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLU | NM_001831.4 | c.705C>T | p.Tyr235= | synonymous_variant | 5/9 | ENST00000316403.15 | |
CLU | NR_038335.2 | n.960C>T | non_coding_transcript_exon_variant | 5/9 | |||
CLU | NR_045494.1 | n.885C>T | non_coding_transcript_exon_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLU | ENST00000316403.15 | c.705C>T | p.Tyr235= | synonymous_variant | 5/9 | 1 | NM_001831.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152042Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251486Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135916
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GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461892Hom.: 0 Cov.: 36 AF XY: 0.0000234 AC XY: 17AN XY: 727246
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GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152042Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74258
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at