rs774882572

Variant names:

• chr4-165333549-C-A
• rs774882572
• NM_006745.5:c.179C>A

Your query was ambiguous. Multiple possible variants found:

• chr4-165333549-C-A
• chr4-165333549-C-G
• chr4-165333549-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_006745.5(MSMO1):​c.179C>A​(p.Ala60Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MSMO1 NM_006745.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.13956803).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSMO1	NM_006745.5	c.179C>A	p.Ala60Asp	missense_variant	Exon 2 of 6	ENST00000261507.11	NP_006736.1
MSMO1	XM_005263176.3	c.179C>A	p.Ala60Asp	missense_variant	Exon 2 of 6		XP_005263233.1
MSMO1	NM_001017369.3	c.-138-4240C>A		intron_variant	Intron 1 of 4		NP_001017369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSMO1	ENST00000261507.11	c.179C>A	p.Ala60Asp	missense_variant	Exon 2 of 6	1	NM_006745.5	ENSP00000261507.6

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Benign	-0.049	T
BayesDel_noAF	Benign	-0.31
CADD	Benign	11
DANN	Benign	0.75
DEOGEN2	Uncertain	0.48	T;T;T;.
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.1
FATHMM_MKL	Benign	0.18	N
LIST_S2	Benign	0.81	T;T;T;T
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.14	T;T;T;T
MetaSVM	Benign	-0.91	T
MutationAssessor	Benign	1.7	L;.;.;.
PrimateAI	Benign	0.31	T
PROVEAN	Uncertain	-3.0	D;D;D;D
REVEL	Benign	0.25
Sift	Uncertain	0.0070	D;D;D;T
Sift4G	Uncertain	0.0070	D;D;D;T
Polyphen		0.055	B;.;B;.
Vest4		0.55
MutPred		0.53		Loss of helix (P = 0.2022);Loss of helix (P = 0.2022);Loss of helix (P = 0.2022);Loss of helix (P = 0.2022);
MVP		0.16
MPC		0.48
ClinPred		0.16	T
GERP RS		-4.6
Varity_R		0.31
gMVP		0.88

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

Other links and lift over

dbSNP: rs774882572; hg19: chr4-166254701;