chr8-31087802-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000553.6(WRN):āc.1458G>Cā(p.Thr486=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,350 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. T486T) has been classified as Likely benign.
Frequency
Consequence
NM_000553.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WRN | NM_000553.6 | c.1458G>C | p.Thr486= | synonymous_variant | 12/35 | ENST00000298139.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WRN | ENST00000298139.7 | c.1458G>C | p.Thr486= | synonymous_variant | 12/35 | 1 | NM_000553.6 | P1 | |
WRN | ENST00000521620.5 | n.159G>C | non_coding_transcript_exon_variant | 1/23 | 1 | ||||
WRN | ENST00000650667.1 | c.*1072G>C | 3_prime_UTR_variant, NMD_transcript_variant | 11/34 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000718 AC: 18AN: 250776Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135542
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461284Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726976
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74282
ClinVar
Submissions by phenotype
Werner syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at