Genetic Variant MOV10L1:c.2627+22C>A (chr22-50145832-C-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.2627+22C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 1,612,350 control chromosomes in the GnomAD database, including 2,205 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 0.056 ( 303 hom., cov: 32)

Exomes 𝑓: 0.049 ( 1902 hom. )

Consequence

MOV10L1
NM_018995.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.12

Publications

5 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=-0.83).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0839 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.2627+22C>A	intron	N/A	NP_061868.1	Q9BXT6-1
MOV10L1	NM_001164104.2		c.2627+22C>A	intron	N/A	NP_001157576.1	Q9BXT6-4
MOV10L1	NM_001164105.2		c.2567+22C>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.2627+22C>A	intron	N/A	ENSP00000262794.5	Q9BXT6-1
MOV10L1	ENST00000395858.7	TSL:1	c.2627+22C>A	intron	N/A	ENSP00000379199.3	Q9BXT6-4
MOV10L1	ENST00000540615.5	TSL:2	c.2567+22C>A	intron	N/A	ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes

AF:

0.0561

AC:

8540

AN:

152168

Hom.:

302

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0861

Gnomad AMI

AF:

0.0537

Gnomad AMR

AF:

0.0272

Gnomad ASJ

AF:

0.0207

Gnomad EAS

AF:

0.0191

Gnomad SAS

AF:

0.0610

Gnomad FIN

AF:

0.0526

Gnomad MID

AF:

0.0191

Gnomad NFE

AF:

0.0496

Gnomad OTH

AF:

0.0478

GnomAD2 exomes

AF:

0.0442

AC:

11066

AN:

250416

AF XY:

0.0449

show subpopulations

Gnomad AFR exome

AF:

0.0909

Gnomad AMR exome

AF:

0.0172

Gnomad ASJ exome

AF:

0.0187

Gnomad EAS exome

AF:

0.0160

Gnomad FIN exome

AF:

0.0529

Gnomad NFE exome

AF:

0.0481

Gnomad OTH exome

AF:

0.0421

GnomAD4 exome

AF:

0.0492

AC:

71879

AN:

1460066

Hom.:

1902

Cov.:

AF XY:

0.0493

AC XY:

35801

AN XY:

726330

show subpopulations

African (AFR)

AF:

0.0904

AC:

3025

AN:

33454

American (AMR)

AF:

0.0182

AC:

814

AN:

44694

Ashkenazi Jewish (ASJ)

AF:

0.0188

AC:

490

AN:

26122

East Asian (EAS)

AF:

0.0126

AC:

500

AN:

39688

South Asian (SAS)

AF:

0.0554

AC:

4778

AN:

86208

European-Finnish (FIN)

AF:

0.0538

AC:

2840

AN:

52748

Middle Eastern (MID)

AF:

0.0329

AC:

172

AN:

5230

European-Non Finnish (NFE)

AF:

0.0508

AC:

56486

AN:

1111612

Other (OTH)

AF:

0.0460

AC:

2774

AN:

60310

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

3320

6640

9959

13279

16599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2142

4284

6426

8568

10710

<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:

0.0562

AC:

8552

AN:

152284

Hom.:

303

Cov.:

AF XY:

0.0549

AC XY:

4087

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.0862

AC:

3583

AN:

41548

American (AMR)

AF:

0.0272

AC:

416

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0207

AC:

AN:

3472

East Asian (EAS)

AF:

0.0188

AC:

AN:

5172

South Asian (SAS)

AF:

0.0607

AC:

293

AN:

4830

European-Finnish (FIN)

AF:

0.0526

AC:

558

AN:

10618

Middle Eastern (MID)

AF:

0.0205

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0497

AC:

3378

AN:

68022

Other (OTH)

AF:

0.0473

AC:

100

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

404

809

1213

1618

2022

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

294

392

490

<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:

0.0288

Hom.:

Bravo

AF:

0.0547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.17

(source)

DANN

Benign

0.55

PhyloP100

-2.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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