X-9891070-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001649.4(SHROOM2):c.411C>T(p.Thr137Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00647 in 1,203,896 control chromosomes in the GnomAD database, including 190 homozygotes. There are 2,863 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001649.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0112 AC: 1256AN: 112552Hom.: 21 Cov.: 25 AF XY: 0.0116 AC XY: 403AN XY: 34680
GnomAD3 exomes AF: 0.0150 AC: 2449AN: 163359Hom.: 87 AF XY: 0.0142 AC XY: 742AN XY: 52111
GnomAD4 exome AF: 0.00599 AC: 6534AN: 1091292Hom.: 169 Cov.: 35 AF XY: 0.00686 AC XY: 2455AN XY: 357958
GnomAD4 genome AF: 0.0112 AC: 1260AN: 112604Hom.: 21 Cov.: 25 AF XY: 0.0117 AC XY: 408AN XY: 34742
ClinVar
Submissions by phenotype
SHROOM2-related disorder Benign:1
This variant is classified as 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