11-838542-C-T

Variant names:

• chr11-838542-C-T
• rs1130698
• NM_004357.5:c.*350C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004357.5(CD151):​c.*350C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 372,882 control chromosomes in the GnomAD database, including 84,704 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.66 (33908 hom., cov: 34)
  • Exomes 𝑓: 0.67 (50796 hom.)
• Consequence: CD151 NM_004357.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959
• Publications: 21 publications found

Genes affected

CD151 (HGNC:1630): (CD151 molecule (Raph blood group)) The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein that is known to complex with integrins and other transmembrane 4 superfamily proteins. It is involved in cellular processes including cell adhesion and may regulate integrin trafficking and/or function. This protein enhances cell motility, invasion and metastasis of cancer cells. Multiple alternatively spliced transcript variants that encode the same protein have been described for this gene. [provided by RefSeq, Jul 2008]

POLR2L (HGNC:9199): (RNA polymerase II, I and III subunit L) This gene encodes a subunit of RNA polymerase II, the polymerase responsible for synthesizing messenger RNA in eukaryotes. The product of this gene contains four conserved cysteines characteristic of an atypical zinc-binding domain. Like its counterpart in yeast, this subunit may be shared by the other two DNA-directed RNA polymerases. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD151	NM_004357.5	c.*350C>T		3_prime_UTR_variant	Exon 9 of 9	ENST00000397420.9	NP_004348.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD151	ENST00000397420.9	c.*350C>T		3_prime_UTR_variant	Exon 9 of 9	1	NM_004357.5	ENSP00000380565.3

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100426 AN: 151954 Hom.: 33896 Cov.: 34

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.898

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.628

GnomAD4 exome AF: 0.666 AC: 147123 AN: 220810 Hom.: 50796 Cov.: 0 AF XY: 0.651 AC XY: 75680 AN XY: 116220

African (AFR) AF: 0.550 AC: 3924 AN: 7132

American (AMR) AF: 0.779 AC: 5793 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 3523 AN: 7254

East Asian (EAS) AF: 0.924 AC: 12703 AN: 13744

South Asian (SAS) AF: 0.475 AC: 11964 AN: 25206

European-Finnish (FIN) AF: 0.742 AC: 9140 AN: 12324

Middle Eastern (MID) AF: 0.511 AC: 510 AN: 998

European-Non Finnish (NFE) AF: 0.682 AC: 91172 AN: 133766

Other (OTH) AF: 0.648 AC: 8394 AN: 12952

GnomAD4 genome AF: 0.661 AC: 100466 AN: 152072 Hom.: 33908 Cov.: 34 AF XY: 0.661 AC XY: 49122 AN XY: 74340

African (AFR) AF: 0.563 AC: 23317 AN: 41450

American (AMR) AF: 0.734 AC: 11228 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1688 AN: 3472

East Asian (EAS) AF: 0.898 AC: 4641 AN: 5166

South Asian (SAS) AF: 0.485 AC: 2343 AN: 4826

European-Finnish (FIN) AF: 0.750 AC: 7962 AN: 10618

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47127 AN: 67934

Other (OTH) AF: 0.630 AC: 1329 AN: 2110

Alfa AF: 0.668 Hom.: 45743

Bravo AF: 0.661

Asia WGS AF: 0.690 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.56
PhyloP100		-0.96
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1130698; hg19: chr11-838542;