chr10-48978370-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001394531.1(WDFY4):c.9353C>A(p.Pro3118Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000111 in 1,550,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001394531.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WDFY4 | NM_001394531.1 | c.9353C>A | p.Pro3118Gln | missense_variant | 60/62 | ENST00000325239.12 | NP_001381460.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WDFY4 | ENST00000325239.12 | c.9353C>A | p.Pro3118Gln | missense_variant | 60/62 | 5 | NM_001394531.1 | ENSP00000320563.5 |
Frequencies
GnomAD3 genomes AF: 0.000434 AC: 66AN: 151932Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000914 AC: 14AN: 153094Hom.: 0 AF XY: 0.0000739 AC XY: 6AN XY: 81236
GnomAD4 exome AF: 0.0000758 AC: 106AN: 1398938Hom.: 0 Cov.: 48 AF XY: 0.0000580 AC XY: 40AN XY: 690006
GnomAD4 genome AF: 0.000434 AC: 66AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74304
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at