9-14886-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001378090.1(WASHC1):c.1319G>A(p.Arg440His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000875 in 1,359,608 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R440C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378090.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WASHC1 | NM_001378090.1 | c.1319G>A | p.Arg440His | missense_variant | Exon 11 of 11 | ENST00000696149.1 | NP_001365019.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WASHC1 | ENST00000696149.1 | c.1319G>A | p.Arg440His | missense_variant | Exon 11 of 11 | NM_001378090.1 | ENSP00000512441.1 | |||
WASHC1 | ENST00000442898.5 | c.1319G>A | p.Arg440His | missense_variant | Exon 11 of 11 | 2 | ENSP00000485627.1 |
Frequencies
GnomAD3 genomes AF: 0.000474 AC: 59AN: 124538Hom.: 2 Cov.: 24
GnomAD3 exomes AF: 0.0000436 AC: 8AN: 183546Hom.: 0 AF XY: 0.0000600 AC XY: 6AN XY: 100052
GnomAD4 exome AF: 0.0000486 AC: 60AN: 1235020Hom.: 3 Cov.: 37 AF XY: 0.0000454 AC XY: 28AN XY: 616490
GnomAD4 genome AF: 0.000474 AC: 59AN: 124588Hom.: 2 Cov.: 24 AF XY: 0.000527 AC XY: 32AN XY: 60700
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1319G>A (p.R440H) alteration is located in exon 11 (coding exon 10) of the WASH1 gene. This alteration results from a G to A substitution at nucleotide position 1319, causing the arginine (R) at amino acid position 440 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at