Genetic Variant MOV10L1:p.Arg182Cys (chr22-50108237-C-T) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_018995.3(MOV10L1):c.544C>T(p.Arg182Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 1,612,090 control chromosomes in the GnomAD database, including 48,249 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.22 ( 4207 hom., cov: 32)

Exomes 𝑓: 0.24 ( 44042 hom. )

Consequence

MOV10L1
NM_018995.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 2.70

Variant links:

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]

MOV10L1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 22-50108237-C-T is Benign according to our data. Variant chr22-50108237-C-T is described in ClinVar as [Benign]. Clinvar id is 1238404.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.544C>T	p.Arg182Cys	missense_variant	Exon 4 of 27	ENST00000262794.10	NP_061868.1	Q9BXT6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10 link	c.544C>T	p.Arg182Cys	missense_variant	Exon 4 of 27	1	NM_018995.3	ENSP00000262794.5		Q9BXT6-1

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34121

AN:

152000

Hom.:

4193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.155

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.351

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.206

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.264

GnomAD3 exomes

AF:

0.266

AC:

65929

AN:

248206

Hom.:

9437

AF XY:

0.266

AC XY:

35710

AN XY:

134336

show subpopulations

Gnomad AFR exome

AF:

0.156

Gnomad AMR exome

AF:

0.409

Gnomad ASJ exome

AF:

0.247

Gnomad EAS exome

AF:

0.273

Gnomad SAS exome

AF:

0.318

Gnomad FIN exome

AF:

0.202

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.242

AC:

353395

AN:

1459972

Hom.:

44042

Cov.:

AF XY:

0.244

AC XY:

177415

AN XY:

726202

show subpopulations

Gnomad4 AFR exome

AF:

0.158

Gnomad4 AMR exome

AF:

0.407

Gnomad4 ASJ exome

AF:

0.241

Gnomad4 EAS exome

AF:

0.281

Gnomad4 SAS exome

AF:

0.315

Gnomad4 FIN exome

AF:

0.203

Gnomad4 NFE exome

AF:

0.233

Gnomad4 OTH exome

AF:

0.245

GnomAD4 genome

AF:

0.225

AC:

34164

AN:

152118

Hom.:

4207

Cov.:

AF XY:

0.226

AC XY:

16790

AN XY:

74352

show subpopulations

Gnomad4 AFR

AF:

0.155

Gnomad4 AMR

AF:

0.352

Gnomad4 ASJ

AF:

0.254

Gnomad4 EAS

AF:

0.267

Gnomad4 SAS

AF:

0.316

Gnomad4 FIN

AF:

0.188

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.271

Alfa

AF:

0.235

Hom.:

10573

Bravo

AF:

0.235

TwinsUK

AF:

0.240

AC:

891

ALSPAC

AF:

0.239

AC:

921

ESP6500AA

AF:

0.151

AC:

665

ESP6500EA

AF:

0.239

AC:

2052

ExAC

AF:

0.262

AC:

31758

Asia WGS

AF:

0.300

AC:

1043

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 24, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.30

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Uncertain

0.59

D;D;.;.

Eigen

Uncertain

0.57

Eigen_PC

Uncertain

0.51

FATHMM_MKL

Uncertain

0.86

LIST_S2

Benign

0.70

T;.;T;T

MetaRNN

Benign

0.0031

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.8

M;M;M;.

PrimateAI

Uncertain

0.58

PROVEAN

Pathogenic

-5.4

D;D;D;D

REVEL

Benign

0.18

Sift

Pathogenic

0.0

D;D;D;D

Sift4G

Pathogenic

0.0

D;D;D;D

Polyphen

1.0

D;D;.;.

Vest4

0.22

MPC

0.52

ClinPred

0.030

GERP RS

4.2

Varity_R

0.61

gMVP

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.53

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.53

Position offset: -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