chrX-50596855-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1441C) has been classified as Uncertain significance.
Frequency
Consequence
NM_020717.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM4 | NM_020717.5 | c.4322G>A | p.Arg1441His | missense_variant | 9/9 | ENST00000376020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4322G>A | p.Arg1441His | missense_variant | 9/9 | 2 | NM_020717.5 | P1 | |
SHROOM4 | ENST00000289292.11 | c.4322G>A | p.Arg1441His | missense_variant | 9/10 | 1 | P1 | ||
SHROOM4 | ENST00000460112.3 | c.3974G>A | p.Arg1325His | missense_variant | 8/8 | 5 |
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
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Aug 02, 2019 | 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