X-50596825-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PP3_StrongBS2
The NM_020717.5(SHROOM4):āc.4352A>Gā(p.Tyr1451Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000273 in 1,209,757 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020717.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4352A>G | p.Tyr1451Cys | missense_variant | Exon 9 of 9 | 2 | NM_020717.5 | ENSP00000365188.2 | ||
SHROOM4 | ENST00000289292.11 | c.4352A>G | p.Tyr1451Cys | missense_variant | Exon 9 of 10 | 1 | ENSP00000289292.7 | |||
SHROOM4 | ENST00000460112.3 | c.4004A>G | p.Tyr1335Cys | missense_variant | Exon 8 of 8 | 5 | ENSP00000421450.1 |
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112451Hom.: 0 Cov.: 24 AF XY: 0.0000289 AC XY: 1AN XY: 34595
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182409Hom.: 0 AF XY: 0.0000299 AC XY: 2AN XY: 66949
GnomAD4 exome AF: 0.0000283 AC: 31AN: 1097306Hom.: 0 Cov.: 31 AF XY: 0.0000276 AC XY: 10AN XY: 362766
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112451Hom.: 0 Cov.: 24 AF XY: 0.0000289 AC XY: 1AN XY: 34595
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4352A>G (p.Y1451C) alteration is located in exon 9 (coding exon 9) of the SHROOM4 gene. This alteration results from a A to G substitution at nucleotide position 4352, causing the tyrosine (Y) at amino acid position 1451 to be replaced by a cysteine (C). 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