6-44390147-T-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001253.4(CDC5L):c.46-121T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.997 in 621,616 control chromosomes in the GnomAD database, including 309,243 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.99 ( 75012 hom., cov: 30)
Exomes 𝑓: 1.0 ( 234231 hom. )
Consequence
CDC5L
NM_001253.4 intron
NM_001253.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.24
Genes affected
CDC5L (HGNC:1743): (cell division cycle 5 like) The protein encoded by this gene shares a significant similarity with Schizosaccharomyces pombe cdc5 gene product, which is a cell cycle regulator important for G2/M transition. This protein has been demonstrated to act as a positive regulator of cell cycle G2/M progression. It was also found to be an essential component of a non-snRNA spliceosome, which contains at least five additional protein factors and is required for the second catalytic step of pre-mRNA splicing. [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=-0.94).
BP6
Variant 6-44390147-T-G is Benign according to our data. Variant chr6-44390147-T-G is described in ClinVar as [Benign]. Clinvar id is 1237785.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDC5L | NM_001253.4 | c.46-121T>G | intron_variant | ENST00000371477.4 | NP_001244.1 | |||
POLR1C | NM_001318876.2 | c.946-51743T>G | intron_variant | NP_001305805.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDC5L | ENST00000371477.4 | c.46-121T>G | intron_variant | 1 | NM_001253.4 | ENSP00000360532 | P1 |
Frequencies
GnomAD3 genomes AF: 0.993 AC: 151003AN: 152116Hom.: 74958 Cov.: 30
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GnomAD4 exome AF: 0.999 AC: 468918AN: 469382Hom.: 234231 AF XY: 0.999 AC XY: 250799AN XY: 251010
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GnomAD4 genome AF: 0.993 AC: 151116AN: 152234Hom.: 75012 Cov.: 30 AF XY: 0.993 AC XY: 73912AN XY: 74418
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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 | GeneDx | Jun 18, 2021 | - - |
Computational scores
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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