chr11-836008-T-C

Variant names:

• chr11-836008-T-C
• rs5030778
• NM_004357.5:c.-7-55T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong 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, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.47
• Publications: 19 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]

CD151 Gene-Disease associations (from GenCC):

• epidermolysis bullosa simplex 7, with nephropathy and deafness

  Inheritance: AR, Unknown Classification: STRONG, MODERATE, SUPPORTIVE, LIMITED Submitted by: Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -20 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 VariationId is 1288975.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004357.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD151	NM_004357.5	MANE Select	c.-7-55T>C		intron	N/A	NP_004348.2
	CD151	NM_001039490.2		c.-7-55T>C		intron	N/A	NP_001034579.1	P48509
	CD151	NM_139029.2		c.-7-55T>C		intron	N/A	NP_620598.1	P48509

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD151	ENST00000397420.9	TSL:1 MANE Select	c.-7-55T>C		intron	N/A	ENSP00000380565.3	P48509
	CD151	ENST00000322008.9	TSL:1	c.-7-55T>C		intron	N/A	ENSP00000324101.4	P48509
	CD151	ENST00000397421.5	TSL:1	c.-7-55T>C		intron	N/A	ENSP00000380566.1	P48509

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

African (AFR) AF: 0.525 AC: 12023 AN: 22882

American (AMR) AF: 0.814 AC: 34211 AN: 42022

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 11087 AN: 22448

East Asian (EAS) AF: 0.891 AC: 32905 AN: 36948

South Asian (SAS) AF: 0.487 AC: 35784 AN: 73508

European-Finnish (FIN) AF: 0.767 AC: 38976 AN: 50846

Middle Eastern (MID) AF: 0.534 AC: 2465 AN: 4616

European-Non Finnish (NFE) AF: 0.695 AC: 422121 AN: 607762

Other (OTH) AF: 0.656 AC: 27586 AN: 42042

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

African (AFR) AF: 0.536 AC: 22229 AN: 41494

American (AMR) AF: 0.733 AC: 11212 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1693 AN: 3472

East Asian (EAS) AF: 0.872 AC: 4521 AN: 5184

South Asian (SAS) AF: 0.484 AC: 2334 AN: 4822

European-Finnish (FIN) AF: 0.767 AC: 8130 AN: 10604

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47229 AN: 68006

Other (OTH) AF: 0.628 AC: 1327 AN: 2114

Alfa AF: 0.676 Hom.: 4369

Bravo AF: 0.651

Asia WGS AF: 0.682 AC: 2371 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.40
PhyloP100		-1.5
PromoterAI		-0.0025	Neutral
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: rs5030778; hg19: chr11-836008;