rs878854893
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The ENST00000320574.10(POLE):c.6505C>T(p.Leu2169=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000413 in 1,454,422 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L2169L) has been classified as Likely benign.
Frequency
Consequence
ENST00000320574.10 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLE | NM_006231.4 | c.6505C>T | p.Leu2169= | synonymous_variant | 46/49 | ENST00000320574.10 | NP_006222.2 | |
POLE | XM_011534795.4 | c.6505C>T | p.Leu2169= | synonymous_variant | 46/48 | XP_011533097.1 | ||
POLE | XM_011534797.4 | c.5584C>T | p.Leu1862= | synonymous_variant | 38/40 | XP_011533099.1 | ||
POLE | XM_011534802.4 | c.3493C>T | p.Leu1165= | synonymous_variant | 22/24 | XP_011533104.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POLE | ENST00000320574.10 | c.6505C>T | p.Leu2169= | synonymous_variant | 46/49 | 1 | NM_006231.4 | ENSP00000322570 | P1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1454422Hom.: 0 Cov.: 32 AF XY: 0.00000415 AC XY: 3AN XY: 722916
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 03, 2024 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2019 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at