22-50092025-G-C

Variant names:

• chr22-50092025-G-C
• rs146070249
• NM_018995.3:c.122G>C

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_018995.3(MOV10L1):​c.122G>C​(p.Arg41Pro) 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. 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. R41Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MOV10L1 NM_018995.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53
• Publications: 0 publications found

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

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.39495373).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3	c.122G>C	p.Arg41Pro	missense_variant	Exon 2 of 27	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10	c.122G>C	p.Arg41Pro	missense_variant	Exon 2 of 27	1	NM_018995.3	ENSP00000262794.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000151

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00 AC: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Benign	0.0050	T
BayesDel_noAF	Benign	-0.23
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.14	T;T;.;.
Eigen	Benign	0.0093
Eigen_PC	Benign	0.019
FATHMM_MKL	Benign	0.50	D
LIST_S2	Benign	0.38	T;.;T;T
M_CAP	Uncertain	0.13	D
MetaRNN	Benign	0.39	T;T;T;T
MetaSVM	Uncertain	-0.082	T
MutationAssessor	Benign	1.1	L;L;L;.
PhyloP100		1.5
PrimateAI	Benign	0.34	T
PROVEAN	Uncertain	-2.7	D;D;D;D
REVEL	Uncertain	0.45
Sift	Benign	0.13	T;T;T;T
Sift4G	Benign	0.10	T;T;T;T
Polyphen		0.97	D;D;.;.
Vest4		0.52
MVP		0.89
MPC		0.39
ClinPred		0.94	D
GERP RS		4.2
Varity_R		0.46
gMVP		0.76
Mutation Taster		=80/20	polymorphism

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

Other links and lift over

dbSNP: rs146070249; hg19: chr22-50530454;