11-836023-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_004357.5(CD151):c.-7-40C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 1,205,144 control chromosomes in the GnomAD database, including 546,414 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.95 (68666 hom., cov: 34)
  • Exomes 𝑓: 0.95 (477748 hom.)
• Consequence: CD151 NM_004357.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.989

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 11-836023-C-T is Benign according to our data. Variant chr11-836023-C-T is described in ClinVar as [Benign]. Clinvar id is 1271751.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD151	NM_004357.5	c.-7-40C>T		intron_variant		ENST00000397420.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD151	ENST00000397420.9	c.-7-40C>T		intron_variant		1	NM_004357.5	P3

Frequencies

GnomAD3 genomes AF: 0.949 AC: 144483 AN: 152216 Hom.: 68603 Cov.: 34

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.983

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.954

GnomAD3 exomes AF: 0.958 AC: 229009 AN: 238996 Hom.: 109749 AF XY: 0.959 AC XY: 124050 AN XY: 129342

Gnomad AFR exome AF: 0.942

Gnomad AMR exome AF: 0.974

Gnomad ASJ exome AF: 0.939

Gnomad EAS exome AF: 1.00

Gnomad SAS exome AF: 0.984

Gnomad FIN exome AF: 0.952

Gnomad NFE exome AF: 0.945

Gnomad OTH exome AF: 0.957

GnomAD4 exome AF: 0.953 AC: 1002819 AN: 1052810 Hom.: 477748 Cov.: 14 AF XY: 0.954 AC XY: 516256 AN XY: 541246

Gnomad4 AFR exome AF: 0.943

Gnomad4 AMR exome AF: 0.974

Gnomad4 ASJ exome AF: 0.942

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.983

Gnomad4 FIN exome AF: 0.952

Gnomad4 NFE exome AF: 0.946

Gnomad4 OTH exome AF: 0.954

GnomAD4 genome AF: 0.949 AC: 144605 AN: 152334 Hom.: 68666 Cov.: 34 AF XY: 0.951 AC XY: 70845 AN XY: 74496

Gnomad4 AFR AF: 0.942

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.983

Gnomad4 FIN AF: 0.949

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.955

Alfa AF: 0.941 Hom.: 7673

Bravo AF: 0.950

Asia WGS AF: 0.988 AC: 3436 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 10, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.39
Dann	Benign	0.56

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

Other links and lift over

dbSNP: rs28475448; hg19: chr11-836023;