rs16826536
Positions:
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001791.4(CDC42):āc.462T>Cā(p.Tyr154=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00404 in 1,613,946 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.013 ( 47 hom., cov: 32)
Exomes š: 0.0031 ( 37 hom. )
Consequence
CDC42
NM_001791.4 synonymous
NM_001791.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0710
Genes affected
CDC42 (HGNC:1736): (cell division cycle 42) The protein encoded by this gene is a small GTPase of the Rho-subfamily, which regulates signaling pathways that control diverse cellular functions including cell morphology, migration, endocytosis and cell cycle progression. This protein is highly similar to Saccharomyces cerevisiae Cdc 42, and is able to complement the yeast cdc42-1 mutant. The product of oncogene Dbl was reported to specifically catalyze the dissociation of GDP from this protein. This protein could regulate actin polymerization through its direct binding to Neural Wiskott-Aldrich syndrome protein (N-WASP), which subsequently activates Arp2/3 complex. Alternative splicing of this gene results in multiple transcript variants. Pseudogenes of this gene have been identified on chromosomes 3, 4, 5, 7, 8 and 20. [provided by RefSeq, Apr 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.53).
BP6
?
Variant 1-22086842-T-C is Benign according to our data. Variant chr1-22086842-T-C is described in ClinVar as [Benign]. Clinvar id is 790477.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.071 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0128 (1957/152296) while in subpopulation AFR AF= 0.0407 (1691/41544). AF 95% confidence interval is 0.0391. There are 47 homozygotes in gnomad4. There are 934 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 1957 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC42 | NM_001791.4 | c.462T>C | p.Tyr154= | synonymous_variant | 5/6 | ENST00000656825.1 | |
CDC42 | NM_001039802.2 | c.462T>C | p.Tyr154= | synonymous_variant | 6/7 | ||
CDC42 | NM_044472.3 | c.462T>C | p.Tyr154= | synonymous_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC42 | ENST00000656825.1 | c.462T>C | p.Tyr154= | synonymous_variant | 5/6 | NM_001791.4 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0128 AC: 1951AN: 152178Hom.: 47 Cov.: 32
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GnomAD3 exomes AF: 0.00478 AC: 1202AN: 251440Hom.: 15 AF XY: 0.00394 AC XY: 536AN XY: 135900
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GnomAD4 exome AF: 0.00312 AC: 4567AN: 1461650Hom.: 37 Cov.: 31 AF XY: 0.00296 AC XY: 2155AN XY: 727138
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GnomAD4 genome ? AF: 0.0129 AC: 1957AN: 152296Hom.: 47 Cov.: 32 AF XY: 0.0125 AC XY: 934AN XY: 74468
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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