rs3216167

Variant names:

• chr8-27604255-CA-C
• rs3216167
• NM_001831.4:c.934+35delT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001831.4(CLU):​c.934+35delT 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891
• Publications: 13 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: Benign. The variant received -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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLU	NM_001831.4	c.934+35delT		intron_variant	Intron 6 of 8	ENST00000316403.15	NP_001822.3
CLU	NR_038335.2	n.1189+35delT		intron_variant	Intron 6 of 8
CLU	NR_045494.1	n.1114+35delT		intron_variant	Intron 6 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLU	ENST00000316403.15	c.934+35delT		intron_variant	Intron 6 of 8	1	NM_001831.4	ENSP00000315130.10

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42458 AN: 151888 Hom.: 6584 Cov.: 20

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

GnomAD2 exomes AF: 0.340 AC: 84489 AN: 248624 AF XY: 0.336

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 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.: 0 AF XY: 0.301 AC XY: 210643 AN XY: 699742

African (AFR) AF: 0.163 AC: 5234 AN: 32186

American (AMR) AF: 0.497 AC: 22156 AN: 44572

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 6556 AN: 25756

East Asian (EAS) AF: 0.428 AC: 16873 AN: 39406

South Asian (SAS) AF: 0.380 AC: 32329 AN: 85062

European-Finnish (FIN) AF: 0.336 AC: 17831 AN: 53038

Middle Eastern (MID) AF: 0.256 AC: 1259 AN: 4920

European-Non Finnish (NFE) AF: 0.282 AC: 298252 AN: 1055942

Other (OTH) AF: 0.295 AC: 17179 AN: 58268

GnomAD4 genome AF: 0.279 AC: 42477 AN: 152006 Hom.: 6590 Cov.: 20 AF XY: 0.286 AC XY: 21264 AN XY: 74292

African (AFR) AF: 0.164 AC: 6825 AN: 41490

American (AMR) AF: 0.400 AC: 6111 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3468

East Asian (EAS) AF: 0.463 AC: 2380 AN: 5144

South Asian (SAS) AF: 0.401 AC: 1930 AN: 4816

European-Finnish (FIN) AF: 0.342 AC: 3608 AN: 10564

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.293 AC: 19918 AN: 67942

Other (OTH) AF: 0.281 AC: 593 AN: 2112

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
PhyloP100		-0.89
Mutation Taster		=100/0	polymorphism (auto)

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: rs3216167; hg19: chr8-27461772; COSMIC: COSV57067062; COSMIC: COSV57067062;