Variant rs9617066 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000262794.10(MOV10L1):c.169A>T(p.Met57Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 1,613,814 control chromosomes in the GnomAD database, including 48,359 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M57T) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.23 ( 4225 hom., cov: 32)

Exomes 𝑓: 0.24 ( 44134 hom. )

Consequence

MOV10L1
ENST00000262794.10 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.002233982).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOV10L1	NM_018995.3 linkuse as main transcript	c.169A>T	p.Met57Leu	missense_variant	2/27	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10 linkuse as main transcript	c.169A>T	p.Met57Leu	missense_variant	2/27	1	NM_018995.3	ENSP00000262794	P1	Q9BXT6-1

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34319

AN:

152016

Hom.:

4210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.350

Gnomad ASJ

AF:

0.254

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.188

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.231

Gnomad OTH

AF:

0.265

GnomAD3 exomes

AF:

0.266

AC:

66890

AN:

251428

Hom.:

9675

AF XY:

0.266

AC XY:

36178

AN XY:

135880

show subpopulations

Gnomad AFR exome

AF:

0.163

Gnomad AMR exome

AF:

0.407

Gnomad ASJ exome

AF:

0.247

Gnomad EAS exome

AF:

0.275

Gnomad SAS exome

AF:

0.319

Gnomad FIN exome

AF:

0.203

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.269

GnomAD4 exome

AF:

0.242

AC:

353974

AN:

1461680

Hom.:

44134

Cov.:

AF XY:

0.244

AC XY:

177709

AN XY:

727156

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.405

Gnomad4 ASJ exome

AF:

0.241

Gnomad4 EAS exome

AF:

0.282

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:

0.226

AC:

34364

AN:

152134

Hom.:

4225

Cov.:

AF XY:

0.227

AC XY:

16911

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.351

Gnomad4 ASJ

AF:

0.254

Gnomad4 EAS

AF:

0.268

Gnomad4 SAS

AF:

0.315

Gnomad4 FIN

AF:

0.188

Gnomad4 NFE

AF:

0.231

Gnomad4 OTH

AF:

0.272

Alfa

AF:

0.227

Hom.:

1356

Bravo

AF:

0.236

TwinsUK

AF:

0.241

AC:

893

ALSPAC

AF:

0.238

AC:

918

ESP6500AA

AF:

0.159

AC:

699

ESP6500EA

AF:

0.238

AC:

2048

ExAC

AF:

0.264

AC:

31990

Asia WGS

AF:

0.301

AC:

1044

AN:

3478

EpiCase

AF:

0.226

EpiControl

AF:

0.232

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.62

BayesDel_noAF

Benign

-0.52

CADD

Benign

3.5

DANN

Benign

0.61

DEOGEN2

Benign

0.040

T;T;.;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.0084

LIST_S2

Benign

0.0084

T;.;T;T

MetaRNN

Benign

0.0022

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-2.2

N;N;N;.

MutationTaster

Benign

1.0

P;P;P;P;P

PrimateAI

Uncertain

0.52

PROVEAN

Benign

0.54

N;N;N;N

REVEL

Benign

0.18

Sift

Benign

1.0

T;T;T;T

Sift4G

Benign

1.0

T;T;T;T

Polyphen

0.0

B;B;.;.

Vest4

0.054

MutPred

0.20

Gain of catalytic residue at M57 (P = 0.0051);Gain of catalytic residue at M57 (P = 0.0051);Gain of catalytic residue at M57 (P = 0.0051);.;

MPC

0.082

ClinPred

0.0012

GERP RS

-0.97

Varity_R

0.053

gMVP

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.060

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

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over