Variant chr4-165341895-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006745.5(MSMO1):c.831G>A(p.Gln277Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0603 in 1,612,140 control chromosomes in the GnomAD database, including 3,225 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.062 ( 342 hom., cov: 32)

Exomes 𝑓: 0.060 ( 2883 hom. )

Consequence

MSMO1
NM_006745.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.174

Variant links:

Genes affected

MSMO1 (HGNC:10545): (methylsterol monooxygenase 1) Sterol-C4-mehtyl oxidase-like protein was isolated based on its similarity to the yeast ERG25 protein. It contains a set of putative metal binding motifs with similarity to that seen in a family of membrane desaturases-hydroxylases. The protein is localized to the endoplasmic reticulum membrane and is believed to function in cholesterol biosynthesis. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MSMO1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 4-165341895-G-A is Benign according to our data. Variant chr4-165341895-G-A is described in ClinVar as [Benign]. Clinvar id is 1229277.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.174 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSMO1	NM_006745.5 linkuse as main transcript	c.831G>A	p.Gln277Gln	synonymous_variant	6/6	ENST00000261507.11	NP_006736.1	Q15800-1
MSMO1	NM_001017369.3 linkuse as main transcript	c.438G>A	p.Gln146Gln	synonymous_variant	5/5		NP_001017369.1	Q15800-2
MSMO1	XM_005263176.3 linkuse as main transcript	c.831G>A	p.Gln277Gln	synonymous_variant	6/6		XP_005263233.1	Q15800-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSMO1	ENST00000261507.11 linkuse as main transcript	c.831G>A	p.Gln277Gln	synonymous_variant	6/6	1	NM_006745.5	ENSP00000261507.6		Q15800-1
MSMO1	ENST00000393766.6 linkuse as main transcript	c.438G>A	p.Gln146Gln	synonymous_variant	5/5	2		ENSP00000377361.2		Q15800-2

Frequencies

GnomAD3 genomes

AF:

0.0621

AC:

9434

AN:

151990

Hom.:

342

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0766

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0340

Gnomad ASJ

AF:

0.0357

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0974

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0625

Gnomad OTH

AF:

0.0532

GnomAD3 exomes

AF:

0.0534

AC:

13409

AN:

251196

Hom.:

494

AF XY:

0.0534

AC XY:

7253

AN XY:

135776

show subpopulations

Gnomad AFR exome

AF:

0.0769

Gnomad AMR exome

AF:

0.0236

Gnomad ASJ exome

AF:

0.0373

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0499

Gnomad FIN exome

AF:

0.0873

Gnomad NFE exome

AF:

0.0637

Gnomad OTH exome

AF:

0.0523

GnomAD4 exome

AF:

0.0601

AC:

87787

AN:

1460032

Hom.:

2883

Cov.:

AF XY:

0.0596

AC XY:

43322

AN XY:

726428

show subpopulations

Gnomad4 AFR exome

AF:

0.0788

Gnomad4 AMR exome

AF:

0.0255

Gnomad4 ASJ exome

AF:

0.0371

Gnomad4 EAS exome

AF:

0.000252

Gnomad4 SAS exome

AF:

0.0506

Gnomad4 FIN exome

AF:

0.0858

Gnomad4 NFE exome

AF:

0.0636

Gnomad4 OTH exome

AF:

0.0560

GnomAD4 genome

AF:

0.0621

AC:

9450

AN:

152108

Hom.:

342

Cov.:

AF XY:

0.0624

AC XY:

4639

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0766

Gnomad4 AMR

AF:

0.0340

Gnomad4 ASJ

AF:

0.0357

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.0441

Gnomad4 FIN

AF:

0.0974

Gnomad4 NFE

AF:

0.0626

Gnomad4 OTH

AF:

0.0559

Alfa

AF:

0.0612

Hom.:

183

Bravo

AF:

0.0578

Asia WGS

AF:

0.0460

AC:

160

AN:

3476

EpiCase

AF:

0.0546

EpiControl

AF:

0.0568

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 09, 2021	- -

MSMO1-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Jul 30, 2019

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

1.0

DANN

Benign

0.41

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over