Variant chr4-165337753-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_006745.5(MSMO1):c.256-36G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0565 in 1,605,226 control chromosomes in the GnomAD database, including 2,935 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.043 ( 205 hom., cov: 33)

Exomes 𝑓: 0.058 ( 2730 hom. )

Consequence

MSMO1
NM_006745.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.267

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:

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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 (BayesDel_noAF=-0.8).

BP6

Variant 4-165337753-G-A is Benign according to our data. Variant chr4-165337753-G-A is described in ClinVar as [Benign]. Clinvar id is 1252181.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
MSMO1	NM_006745.5 linkuse as main transcript	c.256-36G>A	intron_variant	ENST00000261507.11	NP_006736.1
MSMO1	NM_001017369.3 linkuse as main transcript	c.-138-36G>A	intron_variant		NP_001017369.1
MSMO1	XM_005263176.3 linkuse as main transcript	c.256-36G>A	intron_variant		XP_005263233.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
MSMO1	ENST00000261507.11 linkuse as main transcript	c.256-36G>A	intron_variant	1	NM_006745.5	ENSP00000261507	P1	Q15800-1
MSMO1	ENST00000504317.1 linkuse as main transcript	c.256-36G>A	intron_variant	1		ENSP00000423633
MSMO1	ENST00000393766.6 linkuse as main transcript	c.-138-36G>A	intron_variant	2		ENSP00000377361		Q15800-2
MSMO1	ENST00000507013.5 linkuse as main transcript	c.256-36G>A	intron_variant	2		ENSP00000425241

Frequencies

GnomAD3 genomes

AF:

0.0429

AC:

6534

AN:

152190

Hom.:

205

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0110

Gnomad AMI

AF:

0.00658

Gnomad AMR

AF:

0.0251

Gnomad ASJ

AF:

0.0357

Gnomad EAS

AF:

0.000576

Gnomad SAS

AF:

0.0445

Gnomad FIN

AF:

0.0974

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.0623

Gnomad OTH

AF:

0.0340

GnomAD3 exomes

AF:

0.0484

AC:

12106

AN:

250298

Hom.:

432

AF XY:

0.0496

AC XY:

6716

AN XY:

135312

show subpopulations

Gnomad AFR exome

AF:

0.00918

Gnomad AMR exome

AF:

0.0207

Gnomad ASJ exome

AF:

0.0374

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0498

Gnomad FIN exome

AF:

0.0873

Gnomad NFE exome

AF:

0.0634

Gnomad OTH exome

AF:

0.0498

GnomAD4 exome

AF:

0.0579

AC:

84170

AN:

1452918

Hom.:

2730

Cov.:

AF XY:

0.0577

AC XY:

41741

AN XY:

723382

show subpopulations

Gnomad4 AFR exome

AF:

0.00798

Gnomad4 AMR exome

AF:

0.0218

Gnomad4 ASJ exome

AF:

0.0369

Gnomad4 EAS exome

AF:

0.000177

Gnomad4 SAS exome

AF:

0.0504

Gnomad4 FIN exome

AF:

0.0859

Gnomad4 NFE exome

AF:

0.0633

Gnomad4 OTH exome

AF:

0.0514

GnomAD4 genome

AF:

0.0429

AC:

6533

AN:

152308

Hom.:

205

Cov.:

AF XY:

0.0440

AC XY:

3279

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0110

Gnomad4 AMR

AF:

0.0250

Gnomad4 ASJ

AF:

0.0357

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0441

Gnomad4 FIN

AF:

0.0974

Gnomad4 NFE

AF:

0.0623

Gnomad4 OTH

AF:

0.0336

Alfa

AF:

0.0497

Hom.:

Bravo

AF:

0.0353

Asia WGS

AF:

0.0280

AC:

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.1

DANN

Benign

0.77

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