X-50598413-G-A
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_020717.5(SHROOM4):c.4065C>T(p.Ala1355Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,207,709 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000090 ( 0 hom., 0 hem., cov: 22)
Exomes 𝑓: 0.0000073 ( 0 hom. 3 hem. )
Consequence
SHROOM4
NM_020717.5 synonymous
NM_020717.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.87
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 Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant X-50598413-G-A is Benign according to our data. Variant chrX-50598413-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2660554.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-4.87 with no splicing effect.
BS2
High Hemizygotes in GnomAdExome4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SHROOM4 | NM_020717.5 | c.4065C>T | p.Ala1355Ala | synonymous_variant | 8/9 | ENST00000376020.9 | NP_065768.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHROOM4 | ENST00000376020.9 | c.4065C>T | p.Ala1355Ala | synonymous_variant | 8/9 | 2 | NM_020717.5 | ENSP00000365188.2 | ||
SHROOM4 | ENST00000289292.11 | c.4065C>T | p.Ala1355Ala | synonymous_variant | 8/10 | 1 | ENSP00000289292.7 | |||
SHROOM4 | ENST00000460112.3 | c.3717C>T | p.Ala1239Ala | synonymous_variant | 7/8 | 5 | ENSP00000421450.1 |
Frequencies
GnomAD3 genomes AF: 0.00000897 AC: 1AN: 111540Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33722
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GnomAD3 exomes AF: 0.00000565 AC: 1AN: 177128Hom.: 0 AF XY: 0.0000161 AC XY: 1AN XY: 62022
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GnomAD4 exome AF: 0.00000730 AC: 8AN: 1096169Hom.: 0 Cov.: 32 AF XY: 0.00000830 AC XY: 3AN XY: 361653
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GnomAD4 genome AF: 0.00000897 AC: 1AN: 111540Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33722
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | SHROOM4: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at