rs367767415
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005591.4(MRE11):c.2052T>C(p.Val684=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,613,590 control chromosomes in the GnomAD database, including 1 homozygotes. 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. V684V) has been classified as Likely benign.
Frequency
Consequence
NM_005591.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MRE11 | NM_005591.4 | c.2052T>C | p.Val684= | synonymous_variant | 19/20 | ENST00000323929.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MRE11 | ENST00000323929.8 | c.2052T>C | p.Val684= | synonymous_variant | 19/20 | 1 | NM_005591.4 | P3 | |
MRE11 | ENST00000323977.7 | c.1968T>C | p.Val656= | synonymous_variant | 18/19 | 1 | |||
MRE11 | ENST00000407439.7 | c.2061T>C | p.Val687= | synonymous_variant | 19/20 | 2 | |||
MRE11 | ENST00000393241.8 | c.2049T>C | p.Val683= | synonymous_variant | 19/20 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152238Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251354Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135850
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461352Hom.: 1 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727002
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152238Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74388
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 28, 2019 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 23, 2014 | 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. - |
Ataxia-telangiectasia-like disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at