Variant rs3216167 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001831.4(CLU):c.934+35del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.28 ( 6590 hom., cov: 20)

Exomes 𝑓: 0.30 ( 65820 hom. )

Consequence

CLU
NM_001831.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.891

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CLU	NM_001831.4 linkuse as main transcript	c.934+35del	intron_variant	ENST00000316403.15
CLU	NR_038335.2 linkuse as main transcript	n.1189+35del	intron_variant, non_coding_transcript_variant
CLU	NR_045494.1 linkuse as main transcript	n.1114+35del	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLU	ENST00000316403.15 linkuse as main transcript	c.934+35del		intron_variant		1	NM_001831.4	P1	P10909-1

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42458

AN:

151888

Hom.:

6584

Cov.:

show subpopulations

Gnomad AFR

AF:

0.165

Gnomad AMI

AF:

0.212

Gnomad AMR

AF:

0.400

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.400

Gnomad FIN

AF:

0.342

Gnomad MID

AF:

0.293

Gnomad NFE

AF:

0.293

Gnomad OTH

AF:

0.275

GnomAD3 exomes

AF:

0.340

AC:

84489

AN:

248624

Hom.:

15640

AF XY:

0.336

AC XY:

45247

AN XY:

134488

show subpopulations

Gnomad AFR exome

AF:

0.165

Gnomad AMR exome

AF:

0.515

Gnomad ASJ exome

AF:

0.253

Gnomad EAS exome

AF:

0.462

Gnomad SAS exome

AF:

0.386

Gnomad FIN exome

AF:

0.340

Gnomad NFE exome

AF:

0.288

Gnomad OTH exome

AF:

0.319

GnomAD4 exome

AF:

0.299

AC:

417669

AN:

1399150

Hom.:

65820

Cov.:

AF XY:

0.301

AC XY:

210643

AN XY:

699742

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.497

Gnomad4 ASJ exome

AF:

0.255

Gnomad4 EAS exome

AF:

0.428

Gnomad4 SAS exome

AF:

0.380

Gnomad4 FIN exome

AF:

0.336

Gnomad4 NFE exome

AF:

0.282

Gnomad4 OTH exome

AF:

0.295

GnomAD4 genome

AF:

0.279

AC:

42477

AN:

152006

Hom.:

6590

Cov.:

AF XY:

0.286

AC XY:

21264

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.400

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.463

Gnomad4 SAS

AF:

0.401

Gnomad4 FIN

AF:

0.342

Gnomad4 NFE

AF:

0.293

Gnomad4 OTH

AF:

0.281

Alfa

AF:

0.171

Hom.:

742

Bravo

AF:

0.277

Asia WGS

AF:

0.441

AC:

1533

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over