2-173358836-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_031942.5(CDCA7):c.146C>T(p.Thr49Met) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000178 in 1,459,844 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031942.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDCA7 | NM_031942.5 | c.146C>T | p.Thr49Met | missense_variant, splice_region_variant | Exon 2 of 10 | ENST00000306721.8 | NP_114148.3 | |
CDCA7 | NM_145810.3 | c.146C>T | p.Thr49Met | missense_variant, splice_region_variant | Exon 2 of 9 | NP_665809.1 | ||
CDCA7 | XM_047445957.1 | c.146C>T | p.Thr49Met | missense_variant, splice_region_variant | Exon 2 of 6 | XP_047301913.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1459844Hom.: 0 Cov.: 31 AF XY: 0.0000207 AC XY: 15AN XY: 725956
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 49 of the CDCA7 protein (p.Thr49Met). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CDCA7-related conditions. ClinVar contains an entry for this variant (Variation ID: 1519406). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at