X-50598368-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6BP7
The NM_020717.5(SHROOM4):c.4110G>A(p.Gly1370Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000009 in 111,094 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_020717.5 synonymous
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 |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4110G>A | p.Gly1370Gly | synonymous_variant | Exon 8 of 9 | 2 | NM_020717.5 | ENSP00000365188.2 | ||
SHROOM4 | ENST00000289292.11 | c.4110G>A | p.Gly1370Gly | synonymous_variant | Exon 8 of 10 | 1 | ENSP00000289292.7 | |||
SHROOM4 | ENST00000460112.3 | c.3762G>A | p.Gly1254Gly | synonymous_variant | Exon 7 of 8 | 5 | ENSP00000421450.1 |
Frequencies
GnomAD3 genomes AF: 0.00000900 AC: 1AN: 111094Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33310
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.11e-7 AC: 1AN: 1097839Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 1AN XY: 363207
GnomAD4 genome AF: 0.00000900 AC: 1AN: 111094Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33310
ClinVar
Submissions by phenotype
SHROOM4-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at