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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.2627+22C>A		intron_variant	Intron 19 of 26	ENST00000262794.10	NP_061868.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein
MOV10L1	ENST00000262794.10 link	c.2627+22C>A	intron_variant	Intron 19 of 26	1	NM_018995.3	ENSP00000262794.5
MOV10L1	ENST00000395858.7 link	c.2627+22C>A	intron_variant	Intron 19 of 25	1		ENSP00000379199.3
MOV10L1	ENST00000540615.5 link	c.2567+22C>A	intron_variant	Intron 19 of 25	2		ENSP00000438542.1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over