chr17-73285213-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_012121.5(CDC42EP4):c.*217T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 439,882 control chromosomes in the GnomAD database, including 67,365 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.55 ( 22755 hom., cov: 33)
Exomes 𝑓: 0.55 ( 44610 hom. )
Consequence
CDC42EP4
NM_012121.5 3_prime_UTR
NM_012121.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.754
Genes affected
CDC42EP4 (HGNC:17147): (CDC42 effector protein 4) The product of this gene is a member of the CDC42-binding protein family. Members of this family interact with Rho family GTPases and regulate the organization of the actin cytoskeleton. This protein has been shown to bind both CDC42 and TC10 GTPases in a GTP-dependent manner. When overexpressed in fibroblasts, this protein was able to induce pseudopodia formation, which suggested a role in inducing actin filament assembly and cell shape control. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDC42EP4 | NM_012121.5 | c.*217T>C | 3_prime_UTR_variant | 2/2 | ENST00000335793.4 | ||
CDC42EP4 | XM_005257182.3 | c.*217T>C | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDC42EP4 | ENST00000335793.4 | c.*217T>C | 3_prime_UTR_variant | 2/2 | 1 | NM_012121.5 | P1 | ||
CDC42EP4 | ENST00000439510.2 | c.*217T>C | 3_prime_UTR_variant | 3/3 | 2 | ||||
CDC42EP4 | ENST00000581014.1 | c.*245T>C | 3_prime_UTR_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.547 AC: 83108AN: 151944Hom.: 22738 Cov.: 33
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GnomAD4 exome AF: 0.552 AC: 159019AN: 287820Hom.: 44610 Cov.: 3 AF XY: 0.553 AC XY: 81452AN XY: 147176
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GnomAD4 genome AF: 0.547 AC: 83165AN: 152062Hom.: 22755 Cov.: 33 AF XY: 0.554 AC XY: 41203AN XY: 74328
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at