Genetic Variant NM_018995.3:c.2383C>A (chr22-50144121-C-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_018995.3(MOV10L1):c.2383C>A(p.Arg795Arg) variant causes a synonymous change. The variant allele was found at a frequency of 0.19 in 1,609,978 control chromosomes in the GnomAD database, including 31,538 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.19 ( 3019 hom., cov: 33)

Exomes 𝑓: 0.19 ( 28519 hom. )

Consequence

MOV10L1
NM_018995.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.55

Publications

22 publications found

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 was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.2383C>A	p.Arg795Arg	synonymous_variant	Exon 18 of 27	ENST00000262794.10	NP_061868.1	Q9BXT6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
MOV10L1	ENST00000262794.10 link	c.2383C>A	p.Arg795Arg	synonymous_variant	Exon 18 of 27	1	NM_018995.3	ENSP00000262794.5	Q9BXT6-1
MOV10L1	ENST00000395858.7 link	c.2383C>A	p.Arg795Arg	synonymous_variant	Exon 18 of 26	1		ENSP00000379199.3	Q9BXT6-4
MOV10L1	ENST00000540615.5 link	c.2323C>A	p.Arg775Arg	synonymous_variant	Exon 18 of 26	2		ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28754

AN:

152106

Hom.:

3001

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.189

Gnomad AMR

AF:

0.308

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.255

Gnomad SAS

AF:

0.288

Gnomad FIN

AF:

0.160

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.173

Gnomad OTH

AF:

0.206

GnomAD2 exomes

AF:

0.233

AC:

58453

AN:

251206

AF XY:

0.229

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.416

Gnomad ASJ exome

AF:

0.221

Gnomad EAS exome

AF:

0.263

Gnomad FIN exome

AF:

0.177

Gnomad NFE exome

AF:

0.179

Gnomad OTH exome

AF:

0.219

GnomAD4 exome

AF:

0.190

AC:

276586

AN:

1457754

Hom.:

28519

Cov.:

AF XY:

0.192

AC XY:

139313

AN XY:

724388

show subpopulations

African (AFR)

AF:

0.160

AC:

5332

AN:

33422

American (AMR)

AF:

0.407

AC:

18194

AN:

44664

Ashkenazi Jewish (ASJ)

AF:

0.216

AC:

5628

AN:

26080

East Asian (EAS)

AF:

0.264

AC:

10463

AN:

39566

South Asian (SAS)

AF:

0.291

AC:

25045

AN:

86102

European-Finnish (FIN)

AF:

0.177

AC:

9426

AN:

53378

Middle Eastern (MID)

AF:

0.185

AC:

1063

AN:

5748

European-Non Finnish (NFE)

AF:

0.171

AC:

189671

AN:

1108614

Other (OTH)

AF:

0.195

AC:

11764

AN:

60180

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

12024

24048

36073

48097

60121

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6996

13992

20988

27984

34980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.189

AC:

28804

AN:

152224

Hom.:

3019

Cov.:

AF XY:

0.191

AC XY:

14216

AN XY:

74428

show subpopulations

African (AFR)

AF:

0.154

AC:

6395

AN:

41536

American (AMR)

AF:

0.309

AC:

4729

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

813

AN:

3472

East Asian (EAS)

AF:

0.255

AC:

1322

AN:

5176

South Asian (SAS)

AF:

0.289

AC:

1396

AN:

4830

European-Finnish (FIN)

AF:

0.160

AC:

1696

AN:

10596

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.173

AC:

11776

AN:

68008

Other (OTH)

AF:

0.215

AC:

454

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1205

2410

3616

4821

6026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.178

Hom.:

4014

Bravo

AF:

0.201

Asia WGS

AF:

0.285

AC:

988

AN:

3478

EpiCase

AF:

0.165

EpiControl

AF:

0.170

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.18

CADD

Benign

(source)

DANN

Benign

0.88

PhyloP100

4.6

Mutation Taster

=183/117

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.30

Details are displayed if max score is > 0.2

DS_AG_spliceai

0.30

Position offset: 29

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over