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11-836043-C-T

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

2

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

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]

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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 GnomAd at 15 BG gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD151NM_004357.5 linkuse as main transcriptc.-7-20C>T intron_variant ENST00000397420.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD151ENST00000397420.9 linkuse as main transcriptc.-7-20C>T intron_variant 1 NM_004357.5 P3

Frequencies

GnomAD3 genomes
AF:
0.0107
AC:
1634
AN:
152210
Hom.:
15
Cov.:
34
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.:
21
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.:
22
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.:
15
Cov.:
34
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.:
2
Bravo
AF:
0.00996
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingGeneDxOct 20, 2019- -
Epidermolysis bullosa simplex 7, with nephropathy and deafness;C1867341:RAPH BLOOD GROUP SYSTEM Benign:1
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsJan 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.

Other links and lift over

dbSNP: rs192915611; hg19: chr11-836043; API