chr11-835878-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004357.5(CD151):c.-7-185G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.015 in 571,142 control chromosomes in the GnomAD database, including 103 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.013 ( 20 hom., cov: 33)
Exomes 𝑓: 0.016 ( 83 hom. )
Consequence
CD151
NM_004357.5 intron
NM_004357.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.774
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BP6
?
Variant 11-835878-G-A is Benign according to our data. Variant chr11-835878-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1179338.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0128 (1944/152080) while in subpopulation NFE AF= 0.0164 (1116/67998). AF 95% confidence interval is 0.0156. There are 20 homozygotes in gnomad4. There are 997 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 BG gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD151 | NM_004357.5 | c.-7-185G>A | intron_variant | ENST00000397420.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD151 | ENST00000397420.9 | c.-7-185G>A | intron_variant | 1 | NM_004357.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0128 AC: 1945AN: 151960Hom.: 20 Cov.: 33
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GnomAD4 exome AF: 0.0158 AC: 6623AN: 419062Hom.: 83 Cov.: 2 AF XY: 0.0162 AC XY: 3573AN XY: 221220
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GnomAD4 genome ? AF: 0.0128 AC: 1944AN: 152080Hom.: 20 Cov.: 33 AF XY: 0.0134 AC XY: 997AN XY: 74330
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 07, 2020 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at