dbSNP rs28475448: CD151:c.-7-40C>T (chr11-836023-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004357.5(CD151):c.-7-40C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.952 in 1,205,144 control chromosomes in the GnomAD database, including 546,414 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.95 ( 68666 hom., cov: 34)

Exomes 𝑓: 0.95 ( 477748 hom. )

Consequence

CD151
NM_004357.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.989

Publications

14 publications found

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 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

CD151 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 11-836023-C-T is Benign according to our data. Variant chr11-836023-C-T is described in ClinVar as Benign. ClinVar VariationId is 1271751.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD151	NM_004357.5	MANE Select	c.-7-40C>T	intron	N/A	NP_004348.2
CD151	NM_001039490.2		c.-7-40C>T	intron	N/A	NP_001034579.1	P48509
CD151	NM_139029.2		c.-7-40C>T	intron	N/A	NP_620598.1	P48509

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD151	ENST00000397420.9	TSL:1 MANE Select	c.-7-40C>T	intron	N/A	ENSP00000380565.3	P48509
CD151	ENST00000322008.9	TSL:1	c.-7-40C>T	intron	N/A	ENSP00000324101.4	P48509
CD151	ENST00000397421.5	TSL:1	c.-7-40C>T	intron	N/A	ENSP00000380566.1	P48509

Frequencies

GnomAD3 genomes

AF:

0.949

AC:

144483

AN:

152216

Hom.:

68603

Cov.:

show subpopulations

Gnomad AFR

AF:

0.942

Gnomad AMI

AF:

0.920

Gnomad AMR

AF:

0.961

Gnomad ASJ

AF:

0.939

Gnomad EAS

AF:

1.00

Gnomad SAS

AF:

0.983

Gnomad FIN

AF:

0.949

Gnomad MID

AF:

0.940

Gnomad NFE

AF:

0.946

Gnomad OTH

AF:

0.954

GnomAD2 exomes

AF:

0.958

AC:

229009

AN:

238996

AF XY:

0.959

show subpopulations

Gnomad AFR exome

AF:

0.942

Gnomad AMR exome

AF:

0.974

Gnomad ASJ exome

AF:

0.939

Gnomad EAS exome

AF:

1.00

Gnomad FIN exome

AF:

0.952

Gnomad NFE exome

AF:

0.945

Gnomad OTH exome

AF:

0.957

GnomAD4 exome

AF:

0.953

AC:

1002819

AN:

1052810

Hom.:

477748

Cov.:

AF XY:

0.954

AC XY:

516256

AN XY:

541246

show subpopulations

African (AFR)

AF:

0.943

AC:

24221

AN:

25694

American (AMR)

AF:

0.974

AC:

42278

AN:

43428

Ashkenazi Jewish (ASJ)

AF:

0.942

AC:

22186

AN:

23550

East Asian (EAS)

AF:

1.00

AC:

37752

AN:

37758

South Asian (SAS)

AF:

0.983

AC:

75716

AN:

77058

European-Finnish (FIN)

AF:

0.952

AC:

49078

AN:

51528

Middle Eastern (MID)

AF:

0.943

AC:

4626

AN:

4908

European-Non Finnish (NFE)

AF:

0.946

AC:

702016

AN:

741790

Other (OTH)

AF:

0.954

AC:

44946

AN:

47096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

2643

5287

7930

10574

13217

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

11832

23664

35496

47328

59160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.949

AC:

144605

AN:

152334

Hom.:

68666

Cov.:

AF XY:

0.951

AC XY:

70845

AN XY:

74496

show subpopulations

African (AFR)

AF:

0.942

AC:

39160

AN:

41574

American (AMR)

AF:

0.961

AC:

14704

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.939

AC:

3261

AN:

3472

East Asian (EAS)

AF:

1.00

AC:

5189

AN:

5190

South Asian (SAS)

AF:

0.983

AC:

4752

AN:

4834

European-Finnish (FIN)

AF:

0.949

AC:

10084

AN:

10624

Middle Eastern (MID)

AF:

0.942

AC:

277

AN:

294

European-Non Finnish (NFE)

AF:

0.946

AC:

64321

AN:

68014

Other (OTH)

AF:

0.955

AC:

2020

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

393

786

1179

1572

1965

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

912

1824

2736

3648

4560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.941

Hom.:

8019

Bravo

AF:

0.950

Asia WGS

AF:

0.988

AC:

3436

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.39

(source)

DANN

Benign

0.56

PhyloP100

-0.99

PromoterAI

0.060

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over