chr22-50090149-G-C

Variant names:

• chr22-50090149-G-C
• NM_018995.3:c.61G>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.61G>C​(p.Glu21Gln) 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. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: MOV10L1 NM_018995.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.388
• 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=0.2906928).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018995.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOV10L1	NM_018995.3	MANE Select	c.61G>C	p.Glu21Gln	missense	Exon 1 of 27	NP_061868.1	Q9BXT6-1
	MOV10L1	NM_001164104.2		c.61G>C	p.Glu21Gln	missense	Exon 1 of 26	NP_001157576.1	Q9BXT6-4
	MOV10L1	NM_001164105.2		c.-327G>C		5_prime_UTR	Exon 1 of 26	NP_001157577.1	Q9BXT6-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOV10L1	ENST00000262794.10	TSL:1 MANE Select	c.61G>C	p.Glu21Gln	missense	Exon 1 of 27	ENSP00000262794.5	Q9BXT6-1
	MOV10L1	ENST00000395858.7	TSL:1	c.61G>C	p.Glu21Gln	missense	Exon 1 of 26	ENSP00000379199.3	Q9BXT6-4
	MOV10L1	ENST00000395854.6	TSL:1	n.61G>C		non_coding_transcript_exon	Exon 1 of 4	ENSP00000379195.2	F2Z2H1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Benign	-0.018	T
BayesDel_noAF	Benign	-0.26
CADD	Benign	12
DANN	Benign	0.80
DEOGEN2	Benign	0.077	T
Eigen	Benign	-0.41
Eigen_PC	Benign	-0.41
FATHMM_MKL	Benign	0.74	D
LIST_S2	Benign	0.52	T
M_CAP	Pathogenic	0.98	D
MetaRNN	Benign	0.29	T
MetaSVM	Uncertain	-0.25	T
MutationAssessor	Uncertain	2.4	M
PhyloP100		0.39
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.25
Sift	Benign	0.031	D
Sift4G	Uncertain	0.025	D
Polyphen		0.038	B
Vest4		0.050
MutPred		0.10		Gain of MoRF binding (P = 0.1123)
MVP		0.88
MPC		0.10
ClinPred		0.14	T
GERP RS		3.7
PromoterAI		0.16	Neutral
Varity_R		0.10
gMVP		0.40
Mutation Taster		=98/2	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

hg19: chr22-50528578;