rs149731264
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020717.5(SHROOM4):c.316C>T(p.Leu106=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000273 in 1,210,200 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., 4 hem., cov: 24)
Exomes 𝑓: 0.000012 ( 0 hom. 2 hem. )
Consequence
SHROOM4
NM_020717.5 synonymous
NM_020717.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 4.08
Genes affected
SHROOM4 (HGNC:29215): (shroom family member 4) This gene encodes a member of the APX/Shroom family, which contain an N-terminal PDZ domain and a C-terminal ASD2 motif. The encoded protein may play a role in cytoskeletal architecture. Mutations in this gene have been linked to the X-linked Stocco dos Santos syndrome characterized by cognitive disabilities. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BS2
?
High Hemizygotes in GnomAd4 at 4 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHROOM4 | NM_020717.5 | c.316C>T | p.Leu106= | synonymous_variant | 3/9 | ENST00000376020.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.316C>T | p.Leu106= | synonymous_variant | 3/9 | 2 | NM_020717.5 | P1 | |
SHROOM4 | ENST00000289292.11 | c.316C>T | p.Leu106= | synonymous_variant | 3/10 | 1 | P1 | ||
SHROOM4 | ENST00000460112.3 | c.-33C>T | 5_prime_UTR_variant | 2/8 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000178 AC: 20AN: 112499Hom.: 0 Cov.: 24 AF XY: 0.000115 AC XY: 4AN XY: 34637
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GnomAD3 exomes AF: 0.0000717 AC: 13AN: 181273Hom.: 0 AF XY: 0.0000303 AC XY: 2AN XY: 65939
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GnomAD4 exome AF: 0.0000118 AC: 13AN: 1097701Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 2AN XY: 363095
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GnomAD4 genome ? AF: 0.000178 AC: 20AN: 112499Hom.: 0 Cov.: 24 AF XY: 0.000115 AC XY: 4AN XY: 34637
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Apr 14, 2017 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at