Genetic Variant MOV10L1:c.2727+10G>A (chr22-50149724-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_018995.3(MOV10L1):c.2727+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,608,630 control chromosomes in the GnomAD database, including 50,022 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 0.23 ( 4350 hom., cov: 32)

Exomes 𝑓: 0.25 ( 45672 hom. )

Consequence

MOV10L1
NM_018995.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.356

Publications

9 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MOV10L1	NM_018995.3	MANE Select	c.2727+10G>A	intron	N/A	NP_061868.1	Q9BXT6-1
MOV10L1	NM_001164104.2		c.2727+10G>A	intron	N/A	NP_001157576.1	Q9BXT6-4
MOV10L1	NM_001164105.2		c.2667+10G>A	intron	N/A	NP_001157577.1	Q9BXT6-5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MOV10L1	ENST00000262794.10	TSL:1 MANE Select	c.2727+10G>A	intron	N/A	ENSP00000262794.5	Q9BXT6-1
MOV10L1	ENST00000395858.7	TSL:1	c.2727+10G>A	intron	N/A	ENSP00000379199.3	Q9BXT6-4
MOV10L1	ENST00000540615.5	TSL:2	c.2667+10G>A	intron	N/A	ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34758

AN:

151988

Hom.:

4335

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.356

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.318

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.272

GnomAD2 exomes

AF:

0.271

AC:

66337

AN:

245022

AF XY:

0.272

show subpopulations

Gnomad AFR exome

AF:

0.161

Gnomad AMR exome

AF:

0.409

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.273

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.241

Gnomad OTH exome

AF:

0.276

GnomAD4 exome

AF:

0.247

AC:

359802

AN:

1456524

Hom.:

45672

Cov.:

AF XY:

0.249

AC XY:

180674

AN XY:

724446

show subpopulations

African (AFR)

AF:

0.163

AC:

5439

AN:

33394

American (AMR)

AF:

0.409

AC:

18058

AN:

44192

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

6457

AN:

26026

East Asian (EAS)

AF:

0.281

AC:

11127

AN:

39604

South Asian (SAS)

AF:

0.323

AC:

27673

AN:

85742

European-Finnish (FIN)

AF:

0.209

AC:

11105

AN:

53190

Middle Eastern (MID)

AF:

0.260

AC:

1453

AN:

5584

European-Non Finnish (NFE)

AF:

0.238

AC:

263410

AN:

1108598

Other (OTH)

AF:

0.251

AC:

15080

AN:

60194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

14080

28160

42240

56320

70400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9158

18316

27474

36632

45790

<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:

0.229

AC:

34802

AN:

152106

Hom.:

4350

Cov.:

AF XY:

0.230

AC XY:

17133

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.159

AC:

6612

AN:

41500

American (AMR)

AF:

0.356

AC:

5448

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

914

AN:

3470

East Asian (EAS)

AF:

0.268

AC:

1387

AN:

5170

South Asian (SAS)

AF:

0.319

AC:

1534

AN:

4812

European-Finnish (FIN)

AF:

0.195

AC:

2065

AN:

10584

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.235

AC:

15987

AN:

67964

Other (OTH)

AF:

0.279

AC:

589

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1361

2722

4083

5444

6805

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.223

Hom.:

1212

Bravo

AF:

0.239

Asia WGS

AF:

0.307

AC:

1065

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

(source)

DANN

Benign

0.32

PhyloP100

-0.36

PromoterAI

0.015

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over