chr8-86457917-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_007013.4(WWP1):c.2395-4C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00413 in 1,611,060 control chromosomes in the GnomAD database, including 16 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 Likely benign (★).
Frequency
Consequence
NM_007013.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WWP1 | ENST00000517970.6 | c.2395-4C>T | splice_region_variant, intron_variant | Intron 21 of 24 | 1 | NM_007013.4 | ENSP00000427793.1 | |||
WWP1 | ENST00000265428.4 | c.2395-4C>T | splice_region_variant, intron_variant | Intron 19 of 22 | 1 | ENSP00000265428.4 |
Frequencies
GnomAD3 genomes AF: 0.00241 AC: 366AN: 151986Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00303 AC: 759AN: 250878Hom.: 1 AF XY: 0.00314 AC XY: 426AN XY: 135616
GnomAD4 exome AF: 0.00431 AC: 6292AN: 1458956Hom.: 15 Cov.: 30 AF XY: 0.00412 AC XY: 2994AN XY: 725906
GnomAD4 genome AF: 0.00241 AC: 366AN: 152104Hom.: 1 Cov.: 32 AF XY: 0.00199 AC XY: 148AN XY: 74366
ClinVar
Submissions by phenotype
not provided Benign:1
WWP1: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at