12-132639295-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BP6
The NM_006231.4(POLE):āc.5382C>Gā(p.Ile1794Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,660 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_006231.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POLE | NM_006231.4 | c.5382C>G | p.Ile1794Met | missense_variant | Exon 40 of 49 | ENST00000320574.10 | NP_006222.2 | |
POLE | XM_011534795.4 | c.5382C>G | p.Ile1794Met | missense_variant | Exon 40 of 48 | XP_011533097.1 | ||
POLE | XM_011534797.4 | c.4461C>G | p.Ile1487Met | missense_variant | Exon 32 of 40 | XP_011533099.1 | ||
POLE | XM_011534802.4 | c.2370C>G | p.Ile790Met | missense_variant | Exon 16 of 24 | XP_011533104.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000798 AC: 20AN: 250656Hom.: 0 AF XY: 0.0000886 AC XY: 12AN XY: 135426
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461532Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727044
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
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The p.I1794M variant (also known as c.5382C>G), located in coding exon 40 of the POLE gene, results from a C to G substitution at nucleotide position 5382. The isoleucine at codon 1794 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -
not provided Benign:2
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not specified Uncertain:1
The p.Ile1794Met variant in POLE has not been previously reported in individuals with colorectal cancer but has been identified in 8/66456 of European chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs368364666). Computational prediction tools and conservation analysis do n ot provide strong support for or against an impact to the protein. In summary, t he clinical significance of the p.Ile1794Met variant is uncertain. -
Colorectal cancer, susceptibility to, 12;C3554576:Facial dysmorphism-immunodeficiency-livedo-short stature syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at