rs368367429
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_000553.6(WRN):c.839+3T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,606,170 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 0.00023 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
WRN
NM_000553.6 splice_donor_region, intron
NM_000553.6 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.01949
2
Clinical Significance
Conservation
PhyloP100: 0.968
Genes affected
WRN (HGNC:12791): (WRN RecQ like helicase) This gene encodes a member of the RecQ subfamily of DNA helicase proteins. The encoded nuclear protein is important in the maintenance of genome stability and plays a role in DNA repair, replication, transcription and telomere maintenance. This protein contains a N-terminal 3' to 5' exonuclease domain, an ATP-dependent helicase domain and RQC (RecQ helicase conserved region) domain in its central region, and a C-terminal HRDC (helicase RNase D C-terminal) domain and nuclear localization signal. Defects in this gene are the cause of Werner syndrome, an autosomal recessive disorder characterized by accelerated aging and an elevated risk for certain cancers. [provided by RefSeq, Aug 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 8-31076290-T-C is Benign according to our data. Variant chr8-31076290-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 528110.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WRN | NM_000553.6 | c.839+3T>C | splice_donor_region_variant, intron_variant | ENST00000298139.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WRN | ENST00000298139.7 | c.839+3T>C | splice_donor_region_variant, intron_variant | 1 | NM_000553.6 | P1 | |||
WRN | ENST00000651642.1 | c.134+3T>C | splice_donor_region_variant, intron_variant | ||||||
WRN | ENST00000650667.1 | c.*453+3T>C | splice_donor_region_variant, intron_variant, NMD_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152054Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000922 AC: 23AN: 249472Hom.: 0 AF XY: 0.0000741 AC XY: 10AN XY: 134974
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GnomAD4 exome AF: 0.000131 AC: 191AN: 1454116Hom.: 0 Cov.: 28 AF XY: 0.000109 AC XY: 79AN XY: 723724
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GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74282
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Werner syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
Computational scores
Source:
Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at