11-836166-C-T

Variant names:

• chr11-836166-C-T
• rs201750899
• NM_004357.5:c.84+13C>T

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP4_Strong BP6_Very_Strong BS2

The NM_004357.5(CD151):​c.84+13C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00264 in 1,595,278 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0020 (0 hom., cov: 34)
  • Exomes 𝑓: 0.0027 (13 hom.)
• Consequence: CD151 NM_004357.5 intron
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.00500
• Publications: 0 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 -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 11-836166-C-T is Benign according to our data. Variant chr11-836166-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 1175013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAdExome4 at 13 AR,Unknown gene

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.84+13C>T		intron	N/A	NP_004348.2
	CD151	NM_001039490.2		c.84+13C>T		intron	N/A	NP_001034579.1	P48509
	CD151	NM_139029.2		c.84+13C>T		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.84+13C>T		intron	N/A	ENSP00000380565.3	P48509
	CD151	ENST00000322008.9	TSL:1	c.84+13C>T		intron	N/A	ENSP00000324101.4	P48509
	CD151	ENST00000397421.5	TSL:1	c.84+13C>T		intron	N/A	ENSP00000380566.1	P48509

Frequencies

GnomAD3 genomes AF: 0.00201 AC: 305 AN: 152058 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.000894

Gnomad AMI AF: 0.0441

Gnomad AMR AF: 0.000589

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00302

Gnomad OTH AF: 0.00192

GnomAD2 exomes AF: 0.00160 AC: 394 AN: 245750 AF XY: 0.00180

Gnomad AFR exome AF: 0.000893

Gnomad AMR exome AF: 0.000291

Gnomad ASJ exome AF: 0.000403

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.000190

Gnomad NFE exome AF: 0.00263

Gnomad OTH exome AF: 0.00116

GnomAD4 exome AF: 0.00271 AC: 3912 AN: 1443100 Hom.: 13 Cov.: 32 AF XY: 0.00276 AC XY: 1983 AN XY: 718656

African (AFR) AF: 0.000603 AC: 20 AN: 33192

American (AMR) AF: 0.000269 AC: 12 AN: 44604

Ashkenazi Jewish (ASJ) AF: 0.000346 AC: 9 AN: 26048

East Asian (EAS) AF: 0.00 AC: 0 AN: 39590

South Asian (SAS) AF: 0.00160 AC: 137 AN: 85794

European-Finnish (FIN) AF: 0.000462 AC: 24 AN: 51970

Middle Eastern (MID) AF: 0.000537 AC: 3 AN: 5584

European-Non Finnish (NFE) AF: 0.00328 AC: 3596 AN: 1096526

Other (OTH) AF: 0.00186 AC: 111 AN: 59792

GnomAD4 genome AF: 0.00200 AC: 305 AN: 152178 Hom.: 0 Cov.: 34 AF XY: 0.00191 AC XY: 142 AN XY: 74408

African (AFR) AF: 0.000891 AC: 37 AN: 41534

American (AMR) AF: 0.000588 AC: 9 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.00124 AC: 6 AN: 4828

European-Finnish (FIN) AF: 0.000283 AC: 3 AN: 10588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00302 AC: 205 AN: 67956

Other (OTH) AF: 0.00190 AC: 4 AN: 2108

Alfa AF: 0.00172 Hom.: 0

Bravo AF: 0.00200

ClinVar

ClinVar submissions

Significance: Benign/Likely benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	3	not provided (3)
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		-0.0050
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=100/0	polymorphism

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: rs201750899; hg19: chr11-836166;