X-153444753-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_080701.4(TREX2):c.678C>T(p.Tyr226=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000931 in 1,192,730 control chromosomes in the GnomAD database, including 3 homozygotes. There are 43 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00011 ( 0 hom., 3 hem., cov: 24)
Exomes 𝑓: 0.000092 ( 3 hom. 40 hem. )
Consequence
TREX2
NM_080701.4 synonymous
NM_080701.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.982
Genes affected
TREX2 (HGNC:12270): (three prime repair exonuclease 2) This gene encodes a nuclear protein with 3' to 5' exonuclease activity. The encoded protein participates in double-stranded DNA break repair, and may interact with DNA polymerase delta. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant X-153444753-G-A is Benign according to our data. Variant chrX-153444753-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2661683.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.982 with no splicing effect.
BS2
High Hemizygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TREX2 | NM_080701.4 | c.678C>T | p.Tyr226= | synonymous_variant | 2/2 | ENST00000370231.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TREX2 | ENST00000370231.3 | c.678C>T | p.Tyr226= | synonymous_variant | 2/2 | 5 | NM_080701.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000106 AC: 12AN: 113096Hom.: 0 Cov.: 24 AF XY: 0.0000851 AC XY: 3AN XY: 35242
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GnomAD3 exomes AF: 0.000106 AC: 15AN: 141262Hom.: 1 AF XY: 0.000158 AC XY: 7AN XY: 44320
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GnomAD4 exome AF: 0.0000917 AC: 99AN: 1079579Hom.: 3 Cov.: 31 AF XY: 0.000113 AC XY: 40AN XY: 352599
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GnomAD4 genome AF: 0.000106 AC: 12AN: 113151Hom.: 0 Cov.: 24 AF XY: 0.0000850 AC XY: 3AN XY: 35307
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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 | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2022 | TREX2: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at