5-132823883-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001172700.2(SHROOM1):c.1778C>T(p.Ala593Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. A593T) has been classified as Likely benign.
Frequency
Consequence
NM_001172700.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM1 | NM_001172700.2 | c.1778C>T | p.Ala593Val | missense_variant | 7/10 | ENST00000378679.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM1 | ENST00000378679.8 | c.1778C>T | p.Ala593Val | missense_variant | 7/10 | 1 | NM_001172700.2 | P2 | |
SHROOM1 | ENST00000319854.7 | c.1778C>T | p.Ala593Val | missense_variant | 4/7 | 1 | A2 | ||
SHROOM1 | ENST00000617339.4 | c.1778C>T | p.Ala593Val | missense_variant | 5/8 | 5 | P2 | ||
SHROOM1 | ENST00000378676.1 | c.1571C>T | p.Ala524Val | missense_variant | 3/6 | 5 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1382134Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 678652
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 23, 2021 | The c.1778C>T (p.A593V) alteration is located in exon 7 (coding exon 4) of the SHROOM1 gene. This alteration results from a C to T substitution at nucleotide position 1778, causing the alanine (A) at amino acid position 593 to be replaced by a valine (V). 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