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
NM_004357.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.147
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 |
---|---|---|---|---|---|---|---|
CD151 | NM_004357.5 | c.-7-20C>T | intron_variant | ENST00000397420.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD151 | ENST00000397420.9 | c.-7-20C>T | intron_variant | 1 | NM_004357.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0107 AC: 1634AN: 152210Hom.: 15 Cov.: 34
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GnomAD3 exomes AF: 0.0111 AC: 2737AN: 246812Hom.: 21 AF XY: 0.0109 AC XY: 1465AN XY: 133884
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GnomAD4 exome AF: 0.0151 AC: 20518AN: 1355196Hom.: 191 Cov.: 22 AF XY: 0.0146 AC XY: 9895AN XY: 679864
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GnomAD4 genome ? AF: 0.0107 AC: 1633AN: 152328Hom.: 15 Cov.: 34 AF XY: 0.0104 AC XY: 776AN XY: 74496
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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 submitter | clinical testing | GeneDx | Oct 20, 2019 | - - |
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
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at