rs2272837

Positions:

• chr22-50144197-A-C
• chr22-50144197-A-G

Variant summary

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

The NM_018995.3(MOV10L1):​c.2459A>C​(p.Gln820Pro) 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. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q820R) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: MOV10L1 NM_018995.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81

Genes affected

MOV10L1 (HGNC:7201): (Mov10 like RNA helicase 1) This gene is similar to a mouse gene that encodes a putative RNA helicase and shows testis-specific expression. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

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=0.13962275).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOV10L1	NM_018995.3	c.2459A>C	p.Gln820Pro	missense_variant	18/27	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10	c.2459A>C	p.Gln820Pro	missense_variant	18/27	1	NM_018995.3	ENSP00000262794.5
MOV10L1	ENST00000395858.7	c.2459A>C	p.Gln820Pro	missense_variant	18/26	1		ENSP00000379199.3
MOV10L1	ENST00000540615.5	c.2399A>C	p.Gln800Pro	missense_variant	18/26	2		ENSP00000438542.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.094
BayesDel_addAF	Benign	-0.033	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	4.5
DANN	Benign	0.74
DEOGEN2	Benign	0.21	T;T;.;.
Eigen	Benign	-1.2
Eigen_PC	Benign	-1.3
FATHMM_MKL	Benign	0.42	N
LIST_S2	Benign	0.19	T;.;T;T
M_CAP	Benign	0.076	D
MetaRNN	Benign	0.14	T;T;T;T
MetaSVM	Benign	-0.78	T
MutationAssessor	Benign	-0.40	N;N;N;.
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.8	N;N;N;N
REVEL	Benign	0.26
Sift	Uncertain	0.014	D;D;D;D
Sift4G	Benign	0.19	T;T;T;T
Polyphen		0.021	B;B;.;.
Vest4		0.18
MutPred		0.51		Gain of sheet (P = 0.0221);Gain of sheet (P = 0.0221);Gain of sheet (P = 0.0221);.;
MVP		0.48
MPC		0.11
ClinPred		0.38	T
GERP RS		-4.2
Varity_R		0.16
gMVP		0.80

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: rs2272837; hg19: chr22-50582626;