11-836008-T-C

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.-7-55T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 1,055,268 control chromosomes in the GnomAD database, including 248,478 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.65 (33333 hom., cov: 34)
  • Exomes 𝑓: 0.68 (215145 hom.)
• Consequence: CD151 NM_004357.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.47

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 11-836008-T-C is Benign according to our data. Variant chr11-836008-T-C is described in ClinVar as [Benign]. Clinvar id is 1288975.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD151	NM_004357.5	c.-7-55T>C		intron_variant		ENST00000397420.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD151	ENST00000397420.9	c.-7-55T>C		intron_variant		1	NM_004357.5	P3

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99464 AN: 152076 Hom.: 33321 Cov.: 34

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.626

GnomAD4 exome AF: 0.683 AC: 617158 AN: 903074 Hom.: 215145 Cov.: 12 AF XY: 0.673 AC XY: 316756 AN XY: 470344

Gnomad4 AFR exome AF: 0.525

Gnomad4 AMR exome AF: 0.814

Gnomad4 ASJ exome AF: 0.494

Gnomad4 EAS exome AF: 0.891

Gnomad4 SAS exome AF: 0.487

Gnomad4 FIN exome AF: 0.767

Gnomad4 NFE exome AF: 0.695

Gnomad4 OTH exome AF: 0.656

GnomAD4 genome AF: 0.654 AC: 99504 AN: 152194 Hom.: 33333 Cov.: 34 AF XY: 0.655 AC XY: 48719 AN XY: 74416

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.872

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.628

Alfa AF: 0.676 Hom.: 4369

Bravo AF: 0.651

Asia WGS AF: 0.682 AC: 2371 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	0.17
Dann	Benign	0.40

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: rs5030778; hg19: chr11-836008;