rs8050128
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000355860.7(WWOX):c.517-3C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 1,581,356 control chromosomes in the GnomAD database, including 166,567 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
ENST00000355860.7 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWOX | NM_016373.4 | c.517-108260C>A | intron_variant | ENST00000566780.6 | |||
WWOX | NM_001291997.2 | c.178-108260C>A | intron_variant | ||||
WWOX | NM_130791.5 | c.517-3C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
WWOX | NR_120436.3 | n.756-3C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWOX | ENST00000566780.6 | c.517-108260C>A | intron_variant | 1 | NM_016373.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.467 AC: 70874AN: 151814Hom.: 16799 Cov.: 32
GnomAD3 exomes AF: 0.449 AC: 109000AN: 242750Hom.: 24955 AF XY: 0.446 AC XY: 58704AN XY: 131484
GnomAD4 exome AF: 0.451 AC: 644353AN: 1429424Hom.: 149745 Cov.: 34 AF XY: 0.449 AC XY: 319603AN XY: 711194
GnomAD4 genome ? AF: 0.467 AC: 70939AN: 151932Hom.: 16822 Cov.: 32 AF XY: 0.464 AC XY: 34454AN XY: 74258
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Apr 20, 2017 | - - |
WWOX-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 21, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at