dbSNP rs2272836: MOV10L1:p.Arg795Arg (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

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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