5-132823032-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001172700.2(SHROOM1):c.2323G>A(p.Glu775Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000413 in 1,599,972 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001172700.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM1 | ENST00000378679.8 | c.2323G>A | p.Glu775Lys | missense_variant | Exon 10 of 10 | 1 | NM_001172700.2 | ENSP00000367950.3 | ||
SHROOM1 | ENST00000319854.7 | c.2308G>A | p.Glu770Lys | missense_variant | Exon 7 of 7 | 1 | ENSP00000324245.3 | |||
SHROOM1 | ENST00000617339.4 | c.2323G>A | p.Glu775Lys | missense_variant | Exon 8 of 8 | 5 | ENSP00000478436.1 | |||
SHROOM1 | ENST00000378676.1 | c.2116G>A | p.Glu706Lys | missense_variant | Exon 6 of 6 | 5 | ENSP00000367947.1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 27AN: 225978Hom.: 0 AF XY: 0.0000802 AC XY: 10AN XY: 124760
GnomAD4 exome AF: 0.0000414 AC: 60AN: 1447610Hom.: 0 Cov.: 31 AF XY: 0.0000333 AC XY: 24AN XY: 720590
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152362Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2323G>A (p.E775K) alteration is located in exon 10 (coding exon 7) of the SHROOM1 gene. This alteration results from a G to A substitution at nucleotide position 2323, causing the glutamic acid (E) at amino acid position 775 to be replaced by a lysine (K). 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