Genetic Variant CLU:p.Asn317His (chr8-27599995-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001831.4(CLU):c.949A>C(p.Asn317His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0115 in 1,613,952 control chromosomes in the GnomAD database, including 1,846 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N317Y) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.061 ( 987 hom., cov: 32)

Exomes 𝑓: 0.0063 ( 859 hom. )

Consequence

CLU
NM_001831.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.89

Publications

20 publications found

Variant links:

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]

CLU links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0014353693).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

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

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
CLU	NM_001831.4	MANE Select	c.949A>C	p.Asn317His	missense	Exon 7 of 9	NP_001822.3
CLU	NR_038335.2		n.1204A>C		non_coding_transcript_exon	Exon 7 of 9
CLU	NR_045494.1		n.1129A>C		non_coding_transcript_exon	Exon 7 of 9

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CLU	ENST00000316403.15	TSL:1 MANE Select	c.949A>C	p.Asn317His	missense	Exon 7 of 9	ENSP00000315130.10	P10909-1
CLU	ENST00000405140.7	TSL:1	c.949A>C	p.Asn317His	missense	Exon 7 of 9	ENSP00000385419.3	P10909-1
CLU	ENST00000523500.5	TSL:1	c.949A>C	p.Asn317His	missense	Exon 6 of 8	ENSP00000429620.1	P10909-1

Frequencies

GnomAD3 genomes

AF:

0.0612

AC:

9312

AN:

152084

Hom.:

985

Cov.:

show subpopulations

Gnomad AFR

AF:

0.213

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0226

Gnomad ASJ

AF:

0.00346

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000838

Gnomad OTH

AF:

0.0446

GnomAD2 exomes

AF:

0.0156

AC:

3927

AN:

251356

AF XY:

0.0113

show subpopulations

Gnomad AFR exome

AF:

0.212

Gnomad AMR exome

AF:

0.00977

Gnomad ASJ exome

AF:

0.00288

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000633

Gnomad OTH exome

AF:

0.00636

GnomAD4 exome

AF:

0.00628

AC:

9185

AN:

1461750

Hom.:

859

Cov.:

AF XY:

0.00535

AC XY:

3894

AN XY:

727202

show subpopulations

African (AFR)

AF:

0.217

AC:

7249

AN:

33434

American (AMR)

AF:

0.0107

AC:

477

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00333

AC:

AN:

26136

East Asian (EAS)

AF:

0.00

AC:

AN:

39698

South Asian (SAS)

AF:

0.000522

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53408

Middle Eastern (MID)

AF:

0.0101

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.000392

AC:

436

AN:

1111936

Other (OTH)

AF:

0.0138

AC:

833

AN:

60388

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

394

788

1183

1577

1971

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

228

456

684

912

1140

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0613

AC:

9330

AN:

152202

Hom.:

987

Cov.:

AF XY:

0.0583

AC XY:

4339

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.213

AC:

8816

AN:

41480

American (AMR)

AF:

0.0225

AC:

344

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.00346

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5184

South Asian (SAS)

AF:

0.00124

AC:

AN:

4824

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000838

AC:

AN:

68024

Other (OTH)

AF:

0.0441

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

381

763

1144

1526

1907

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

164

246

328

410

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0229

Hom.:

684

Bravo

AF:

0.0700

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000778

AC:

ESP6500AA

AF:

0.197

AC:

869

ESP6500EA

AF:

0.00116

AC:

ExAC

AF:

0.0192

AC:

2332

Asia WGS

AF:

0.0130

AC:

AN:

3478

EpiCase

AF:

0.000763

EpiControl

AF:

0.000474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.11

BayesDel_addAF

Benign

-0.65

BayesDel_noAF

Benign

-0.56

CADD

Benign

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.19

Eigen

Benign

-0.45

Eigen_PC

Benign

-0.57

FATHMM_MKL

Benign

0.69

LIST_S2

Benign

0.74

MetaRNN

Benign

0.0014

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.6

PhyloP100

1.9

PrimateAI

Benign

0.34

PROVEAN

Benign

-1.7

REVEL

Benign

0.14

Sift

Uncertain

0.027

Sift4G

Uncertain

0.045

Polyphen

1.0

Vest4

0.077

MPC

1.4

ClinPred

0.027

GERP RS

-1.3

PromoterAI

-0.022

Neutral

(source)

Varity_R

0.046

gMVP

0.23

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over