rs201001790
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_006231.4(POLE):c.5542C>T(p.Leu1848Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000062 in 1,613,976 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L1848V) has been classified as Uncertain significance.
Frequency
Consequence
NM_006231.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLE | NM_006231.4 | c.5542C>T | p.Leu1848Phe | missense_variant | 40/49 | ENST00000320574.10 | |
POLE | XM_011534795.4 | c.5542C>T | p.Leu1848Phe | missense_variant | 40/48 | ||
POLE | XM_011534797.4 | c.4621C>T | p.Leu1541Phe | missense_variant | 32/40 | ||
POLE | XM_011534802.4 | c.2530C>T | p.Leu844Phe | missense_variant | 16/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLE | ENST00000320574.10 | c.5542C>T | p.Leu1848Phe | missense_variant | 40/49 | 1 | NM_006231.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251098Hom.: 1 AF XY: 0.000140 AC XY: 19AN XY: 135670
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461792Hom.: 1 Cov.: 31 AF XY: 0.0000509 AC XY: 37AN XY: 727218
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74358
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at