X-50596855-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_020717.5(SHROOM4):c.4322G>A(p.Arg1441His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,209,366 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020717.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4322G>A | p.Arg1441His | missense_variant | Exon 9 of 9 | 2 | NM_020717.5 | ENSP00000365188.2 | ||
SHROOM4 | ENST00000289292.11 | c.4322G>A | p.Arg1441His | missense_variant | Exon 9 of 10 | 1 | ENSP00000289292.7 | |||
SHROOM4 | ENST00000460112.3 | c.3974G>A | p.Arg1325His | missense_variant | Exon 8 of 8 | 5 | ENSP00000421450.1 |
Frequencies
GnomAD3 genomes AF: 0.00000891 AC: 1AN: 112291Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34461
GnomAD3 exomes AF: 0.0000165 AC: 3AN: 181325Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65973
GnomAD4 exome AF: 0.0000128 AC: 14AN: 1097075Hom.: 0 Cov.: 31 AF XY: 0.00000828 AC XY: 3AN XY: 362505
GnomAD4 genome AF: 0.00000891 AC: 1AN: 112291Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34461
ClinVar
Submissions by phenotype
X-linked intellectual disability, Stocco dos Santos type Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at