17-64477964-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_007215.4(POLG2):c.1317C>T(p.Phe439=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000031 in 1,613,780 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 (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
POLG2
NM_007215.4 synonymous
NM_007215.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.42
Genes affected
POLG2 (HGNC:9180): (DNA polymerase gamma 2, accessory subunit) This gene encodes the processivity subunit of the mitochondrial DNA polymerase gamma. The encoded protein forms a heterotrimer containing one catalytic subunit and two processivity subunits. This protein enhances DNA binding and promotes processive DNA synthesis. Mutations in this gene result in autosomal dominant progressive external ophthalmoplegia with mitochondrial DNA deletions.[provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 17-64477964-G-A is Benign according to our data. Variant chr17-64477964-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1663513.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLG2 | NM_007215.4 | c.1317C>T | p.Phe439= | synonymous_variant | 8/8 | ENST00000539111.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLG2 | ENST00000539111.7 | c.1317C>T | p.Phe439= | synonymous_variant | 8/8 | 1 | NM_007215.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251158Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135756
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461628Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727106
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2022 | - - |
Computational scores
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Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: -5
Find out detailed SpliceAI scores and Pangolin per-transcript scores at