X-50598412-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_020717.5(SHROOM4):​c.4066G>A​(p.Val1356Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000846 in 1,207,779 control chromosomes in the GnomAD database, including 5 homozygotes. There are 279 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0012 ( 1 hom., 36 hem., cov: 22)
Exomes 𝑓: 0.00081 ( 4 hom. 243 hem. )

Consequence

SHROOM4
NM_020717.5 missense

Scores

16

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 0.292
Variant links:
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 -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0037336648).
BP6
Variant X-50598412-C-T is Benign according to our data. Variant chrX-50598412-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 212181.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-50598412-C-T is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000815 (893/1096138) while in subpopulation AMR AF= 0.0194 (680/34995). AF 95% confidence interval is 0.0182. There are 4 homozygotes in gnomad4_exome. There are 243 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Hemizygotes in GnomAd4 at 36 XL gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SHROOM4NM_020717.5 linkc.4066G>A p.Val1356Ile missense_variant Exon 8 of 9 ENST00000376020.9 NP_065768.2 Q9ULL8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SHROOM4ENST00000376020.9 linkc.4066G>A p.Val1356Ile missense_variant Exon 8 of 9 2 NM_020717.5 ENSP00000365188.2 Q9ULL8-1
SHROOM4ENST00000289292.11 linkc.4066G>A p.Val1356Ile missense_variant Exon 8 of 10 1 ENSP00000289292.7 Q9ULL8-1
SHROOM4ENST00000460112.3 linkc.3718G>A p.Val1240Ile missense_variant Exon 7 of 8 5 ENSP00000421450.1 Q9ULL8-2

Frequencies

GnomAD3 genomes
AF:
0.00116
AC:
130
AN:
111589
Hom.:
1
Cov.:
22
AF XY:
0.00107
AC XY:
36
AN XY:
33767
show subpopulations
Gnomad AFR
AF:
0.000359
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00944
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00337
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000752
Gnomad OTH
AF:
0.00266
GnomAD3 exomes
AF:
0.00319
AC:
565
AN:
177184
Hom.:
1
AF XY:
0.00217
AC XY:
135
AN XY:
62098
show subpopulations
Gnomad AFR exome
AF:
0.000393
Gnomad AMR exome
AF:
0.0188
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00259
Gnomad SAS exome
AF:
0.000277
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000254
Gnomad OTH exome
AF:
0.00227
GnomAD4 exome
AF:
0.000815
AC:
893
AN:
1096138
Hom.:
4
Cov.:
32
AF XY:
0.000672
AC XY:
243
AN XY:
361634
show subpopulations
Gnomad4 AFR exome
AF:
0.000303
Gnomad4 AMR exome
AF:
0.0194
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00465
Gnomad4 SAS exome
AF:
0.000205
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000190
Gnomad4 OTH exome
AF:
0.000826
GnomAD4 genome
AF:
0.00116
AC:
129
AN:
111641
Hom.:
1
Cov.:
22
AF XY:
0.00106
AC XY:
36
AN XY:
33829
show subpopulations
Gnomad4 AFR
AF:
0.000358
Gnomad4 AMR
AF:
0.00934
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00338
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000752
Gnomad4 OTH
AF:
0.00263
Alfa
AF:
0.000467
Hom.:
17
Bravo
AF:
0.00189
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000149
AC:
1
ExAC
AF:
0.00227
AC:
275

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Jun 20, 2017
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Dec 31, 2019
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

not specified Benign:2
Feb 09, 2016
Genetic Services Laboratory, University of Chicago
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Mar 01, 2018
Ambry Genetics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

SHROOM4-related disorder Benign:1
Jan 13, 2020
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
-0.79
T
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.4
DANN
Benign
0.69
DEOGEN2
Benign
0.0064
T;T;.
FATHMM_MKL
Benign
0.21
N
LIST_S2
Benign
0.43
T;.;T
MetaRNN
Benign
0.0037
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.4
L;L;.
PrimateAI
Benign
0.33
T
PROVEAN
Benign
-0.51
N;N;N
REVEL
Benign
0.010
Sift
Benign
0.16
T;T;T
Sift4G
Benign
0.32
T;T;T
Polyphen
0.015
B;B;.
Vest4
0.064
MVP
0.12
MPC
0.087
ClinPred
0.0038
T
GERP RS
0.65
Varity_R
0.042
gMVP
0.089

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs137923286; hg19: chrX-50341412; API