Genetic Variant MOV10L1:p.Pro821Pro (chr22-50144201-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_018995.3(MOV10L1):c.2463G>A(p.Pro821Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0594 in 1,610,790 control chromosomes in the GnomAD database, including 3,372 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 0.045 ( 211 hom., cov: 33)

Exomes 𝑓: 0.061 ( 3161 hom. )

Consequence

MOV10L1
NM_018995.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.94

Publications

8 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 -13 ACMG points.

BP4

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

BP7

Synonymous conserved (PhyloP=-3.94 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.2463G>A	p.Pro821Pro	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.2463G>A	p.Pro821Pro	synonymous_variant	Exon 18 of 27	1	NM_018995.3	ENSP00000262794.5	Q9BXT6-1
MOV10L1	ENST00000395858.7 link	c.2463G>A	p.Pro821Pro	synonymous_variant	Exon 18 of 26	1		ENSP00000379199.3	Q9BXT6-4
MOV10L1	ENST00000540615.5 link	c.2403G>A	p.Pro801Pro	synonymous_variant	Exon 18 of 26	2		ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes

AF:

0.0447

AC:

6805

AN:

152200

Hom.:

211

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0109

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0368

Gnomad ASJ

AF:

0.163

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.0275

Gnomad FIN

AF:

0.0327

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.0671

Gnomad OTH

AF:

0.0607

GnomAD2 exomes

AF:

0.0496

AC:

12454

AN:

251076

AF XY:

0.0520

show subpopulations

Gnomad AFR exome

AF:

0.00978

Gnomad AMR exome

AF:

0.0282

Gnomad ASJ exome

AF:

0.154

Gnomad EAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.0356

Gnomad NFE exome

AF:

0.0673

Gnomad OTH exome

AF:

0.0695

GnomAD4 exome

AF:

0.0610

AC:

88910

AN:

1458472

Hom.:

3161

Cov.:

AF XY:

0.0609

AC XY:

44152

AN XY:

724954

show subpopulations

African (AFR)

AF:

0.0108

AC:

361

AN:

33422

American (AMR)

AF:

0.0310

AC:

1387

AN:

44696

Ashkenazi Jewish (ASJ)

AF:

0.149

AC:

3891

AN:

26106

East Asian (EAS)

AF:

0.000101

AC:

AN:

39628

South Asian (SAS)

AF:

0.0312

AC:

2691

AN:

86204

European-Finnish (FIN)

AF:

0.0344

AC:

1826

AN:

53056

Middle Eastern (MID)

AF:

0.126

AC:

725

AN:

5756

European-Non Finnish (NFE)

AF:

0.0668

AC:

74157

AN:

1109372

Other (OTH)

AF:

0.0642

AC:

3868

AN:

60232

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.451

Heterozygous variant carriers

4764

9527

14291

19054

23818

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2680

5360

8040

10720

13400

<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:

0.0447

AC:

6803

AN:

152318

Hom.:

211

Cov.:

AF XY:

0.0426

AC XY:

3170

AN XY:

74484

show subpopulations

African (AFR)

AF:

0.0108

AC:

449

AN:

41570

American (AMR)

AF:

0.0367

AC:

562

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.163

AC:

565

AN:

3468

East Asian (EAS)

AF:

0.000385

AC:

AN:

5190

South Asian (SAS)

AF:

0.0276

AC:

133

AN:

4826

European-Finnish (FIN)

AF:

0.0327

AC:

347

AN:

10612

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0671

AC:

4564

AN:

68030

Other (OTH)

AF:

0.0601

AC:

127

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

332

665

997

1330

1662

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

156

234

312

390

<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:

0.0671

Hom.:

218

Bravo

AF:

0.0449

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.0732

EpiControl

AF:

0.0747

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.036

(source)

DANN

Benign

0.82

PhyloP100

-3.9

Mutation Taster

=292/8

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