rs199923241
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000553.6(WRN):c.835C>A(p.Arg279=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000659 in 151,670 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 (★). Synonymous variant affecting the same amino acid position (i.e. R279R) has been classified as Likely benign.
Frequency
Consequence
NM_000553.6 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WRN | NM_000553.6 | c.835C>A | p.Arg279= | synonymous_variant | 8/35 | ENST00000298139.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WRN | ENST00000298139.7 | c.835C>A | p.Arg279= | synonymous_variant | 8/35 | 1 | NM_000553.6 | P1 | |
WRN | ENST00000651642.1 | c.130C>A | p.Arg44= | synonymous_variant | 2/4 | ||||
WRN | ENST00000650667.1 | c.*449C>A | 3_prime_UTR_variant, NMD_transcript_variant | 7/34 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151670Hom.: 0 Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1459324Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726108
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151670Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74060
ClinVar
Submissions by phenotype
Werner syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at