chr19-29812577-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001238.4(CCNE1):c.22C>T(p.Arg8Trp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000527 in 1,518,260 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001238.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCNE1 | NM_001238.4 | c.22C>T | p.Arg8Trp | missense_variant, splice_region_variant | 2/12 | ENST00000262643.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCNE1 | ENST00000262643.8 | c.22C>T | p.Arg8Trp | missense_variant, splice_region_variant | 2/12 | 1 | NM_001238.4 | P1 | |
CCNE1 | ENST00000575243.5 | c.22C>T | p.Arg8Trp | missense_variant, splice_region_variant | 2/8 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000663 AC: 1AN: 150886Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000512 AC: 7AN: 1367262Hom.: 0 Cov.: 33 AF XY: 0.00000148 AC XY: 1AN XY: 673836
GnomAD4 genome AF: 0.00000662 AC: 1AN: 150998Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73810
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at