NM_001831.4:c.954C>A

Variant names:

• chr8-27599990-G-T
• rs9331937
• NM_001831.4:c.954C>A

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP7

The NM_001831.4(CLU):​c.954C>A​(p.Pro318Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P318P) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CLU NM_001831.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.66
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (REVEL=0.153).
• BP7: Synonymous conserved (PhyloP=-3.66 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001831.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLU	NM_001831.4	MANE Select	c.954C>A	p.Pro318Pro	synonymous	Exon 7 of 9	NP_001822.3
	CLU	NR_038335.2		n.1209C>A		non_coding_transcript_exon	Exon 7 of 9
	CLU	NR_045494.1		n.1134C>A		non_coding_transcript_exon	Exon 7 of 9

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLU	ENST00000316403.15	TSL:1 MANE Select	c.954C>A	p.Pro318Pro	synonymous	Exon 7 of 9	ENSP00000315130.10
	CLU	ENST00000405140.7	TSL:1	c.954C>A	p.Pro318Pro	synonymous	Exon 7 of 9	ENSP00000385419.3
	CLU	ENST00000523500.5	TSL:1	c.954C>A	p.Pro318Pro	synonymous	Exon 6 of 8	ENSP00000429620.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.099
DANN	Benign	0.50
PhyloP100		-3.7
PromoterAI		-0.052	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9331937; hg19: chr8-27457507;