12-132661167-G-GAA
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS1
The NM_006231.4(POLE):c.2865-5_2865-4dupTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000903 in 1,368,040 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00016 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00098 ( 0 hom. )
Consequence
POLE
NM_006231.4 splice_region, intron
NM_006231.4 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.191
Genes affected
POLE (HGNC:9177): (DNA polymerase epsilon, catalytic subunit) This gene encodes the catalytic subunit of DNA polymerase epsilon. The enzyme is involved in DNA repair and chromosomal DNA replication. Mutations in this gene have been associated with colorectal cancer 12 and facial dysmorphism, immunodeficiency, livedo, and short stature. [provided by RefSeq, Sep 2013]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP6
Variant 12-132661167-G-GAA is Benign according to our data. Variant chr12-132661167-G-GAA is described in ClinVar as [Likely_benign]. Clinvar id is 801260.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.000985 (1215/1233756) while in subpopulation SAS AF= 0.0027 (185/68468). AF 95% confidence interval is 0.00238. There are 0 homozygotes in gnomad4_exome. There are 638 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000156 AC: 21AN: 134284Hom.: 0 Cov.: 31
GnomAD3 genomes
AF:
AC:
21
AN:
134284
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.000985 AC: 1215AN: 1233756Hom.: 0 Cov.: 0 AF XY: 0.00104 AC XY: 638AN XY: 612260
GnomAD4 exome
AF:
AC:
1215
AN:
1233756
Hom.:
Cov.:
0
AF XY:
AC XY:
638
AN XY:
612260
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000156 AC: 21AN: 134284Hom.: 0 Cov.: 31 AF XY: 0.000139 AC XY: 9AN XY: 64610
GnomAD4 genome
AF:
AC:
21
AN:
134284
Hom.:
Cov.:
31
AF XY:
AC XY:
9
AN XY:
64610
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital | Aug 15, 2023 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Mar 11, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at