11-835877-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.-7-186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.656 in 566,102 control chromosomes in the GnomAD database, including 124,925 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.64 (31688 hom., cov: 30)
  • Exomes 𝑓: 0.66 (93237 hom.)
• Consequence: CD151 NM_004357.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.325

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=-0.91).
• BP6: Variant 11-835877-C-T is Benign according to our data. Variant chr11-835877-C-T is described in ClinVar as [Benign]. Clinvar id is 1289523.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD151	NM_004357.5	c.-7-186C>T		intron_variant		ENST00000397420.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD151	ENST00000397420.9	c.-7-186C>T		intron_variant		1	NM_004357.5	P3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96998 AN: 151706 Hom.: 31674 Cov.: 30

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 0.662 AC: 274129 AN: 414278 Hom.: 93237 Cov.: 2 AF XY: 0.648 AC XY: 141893 AN XY: 218876

Gnomad4 AFR exome AF: 0.531

Gnomad4 AMR exome AF: 0.739

Gnomad4 ASJ exome AF: 0.487

Gnomad4 EAS exome AF: 0.895

Gnomad4 SAS exome AF: 0.463

Gnomad4 FIN exome AF: 0.720

Gnomad4 NFE exome AF: 0.679

Gnomad4 OTH exome AF: 0.641

GnomAD4 genome AF: 0.639 AC: 97040 AN: 151824 Hom.: 31688 Cov.: 30 AF XY: 0.638 AC XY: 47343 AN XY: 74198

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.615

Alfa AF: 0.663 Hom.: 4184

Bravo AF: 0.638

Asia WGS AF: 0.676 AC: 2347 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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.8
Dann	Benign	0.64

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

Publications

LitVar

Other links and lift over

dbSNP: rs12577801; hg19: chr11-835877;