chrX-50813989-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PVS1_StrongBP6BS2
The NM_020717.5(SHROOM4):āc.30C>Gā(p.Tyr10*) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000116 in 1,206,179 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_020717.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000906 AC: 1AN: 110361Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32631
GnomAD4 exome AF: 0.0000119 AC: 13AN: 1095818Hom.: 0 Cov.: 29 AF XY: 0.00000830 AC XY: 3AN XY: 361304
GnomAD4 genome AF: 0.00000906 AC: 1AN: 110361Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32631
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Variant summary: SHROOM4 c.30C>G (p.Tyr10X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay. The variant was absent in 177854 control chromosomes, however other loss of function variants have been reported in gnomad in a small number of hemizygous individuals. To our knowledge, no occurrence of c.30C>G in individuals affected with X-Linked Intellectual Disability, Stocco Dos Santos Type and no experimental evidence demonstrating its impact on protein function have been reported. One submitter has cited clinical-significance assessments for this variant to ClinVar after 2014 and has classified the variant as likely benign. Due to the association of SHROOM4 with disease not being clearly established the variant was classified as VUS. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at