Variant 11-836043-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004357.5(CD151):c.-7-20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 1,507,524 control chromosomes in the GnomAD database, including 206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.011 ( 15 hom., cov: 34)

Exomes 𝑓: 0.015 ( 191 hom. )

Consequence

CD151
NM_004357.5 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.147

Variant links:

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 links:

CD151 (HGNC:):

CD151 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant 11-836043-C-T is Benign according to our data. Variant chr11-836043-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1223149.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0107 (1633/152328) while in subpopulation NFE AF= 0.016 (1091/68028). AF 95% confidence interval is 0.0152. There are 15 homozygotes in gnomad4. There are 776 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 15 BG gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD151	NM_004357.5 linkuse as main transcript	c.-7-20C>T		intron_variant		ENST00000397420.9	NP_004348.2	P48509A0A024RCB3Q6ZNZ0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD151	ENST00000397420.9 linkuse as main transcript	c.-7-20C>T		intron_variant		1	NM_004357.5	ENSP00000380565.3		P48509

Frequencies

GnomAD3 genomes

AF:

0.0107

AC:

1634

AN:

152210

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00210

Gnomad AMI

AF:

0.00987

Gnomad AMR

AF:

0.0101

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00248

Gnomad FIN

AF:

0.0210

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0161

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.0111

AC:

2737

AN:

246812

Hom.:

AF XY:

0.0109

AC XY:

1465

AN XY:

133884

show subpopulations

Gnomad AFR exome

AF:

0.00267

Gnomad AMR exome

AF:

0.00872

Gnomad ASJ exome

AF:

0.0126

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00322

Gnomad FIN exome

AF:

0.0203

Gnomad NFE exome

AF:

0.0150

Gnomad OTH exome

AF:

0.0126

GnomAD4 exome

AF:

0.0151

AC:

20518

AN:

1355196

Hom.:

191

Cov.:

AF XY:

0.0146

AC XY:

9895

AN XY:

679864

show subpopulations

Gnomad4 AFR exome

AF:

0.00229

Gnomad4 AMR exome

AF:

0.00883

Gnomad4 ASJ exome

AF:

0.0126

Gnomad4 EAS exome

AF:

0.0000255

Gnomad4 SAS exome

AF:

0.00362

Gnomad4 FIN exome

AF:

0.0193

Gnomad4 NFE exome

AF:

0.0173

Gnomad4 OTH exome

AF:

0.0137

GnomAD4 genome

AF:

0.0107

AC:

1633

AN:

152328

Hom.:

Cov.:

AF XY:

0.0104

AC XY:

776

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00209

Gnomad4 AMR

AF:

0.0101

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00249

Gnomad4 FIN

AF:

0.0210

Gnomad4 NFE

AF:

0.0160

Gnomad4 OTH

AF:

0.00804

Alfa

AF:

0.00806

Hom.:

Bravo

AF:

0.00996

Asia WGS

AF:

0.00173

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 20, 2019	- -
Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Epidermolysis bullosa simplex 7, with nephropathy and deafness;C1867341:RAPH BLOOD GROUP SYSTEM

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jan 03, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

9.4

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over