Genetic Variant MOV10L1:p.Asp905Asp (chr22-50149702-C-T) – 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.2715C>T(p.Asp905Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 1,612,424 control chromosomes in the GnomAD database, including 74,670 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 ( 5067 hom., cov: 33)

Exomes 𝑓: 0.30 ( 69603 hom. )

Consequence

MOV10L1
NM_018995.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.342

Publications

17 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=-0.79).

BP7

Synonymous conserved (PhyloP=0.342 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.2715C>T	p.Asp905Asp	synonymous_variant	Exon 20 of 27	ENST00000262794.10	NP_061868.1	Q9BXT6-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOV10L1	ENST00000262794.10 link	c.2715C>T	p.Asp905Asp	synonymous_variant	Exon 20 of 27	1	NM_018995.3	ENSP00000262794.5		Q9BXT6-1

Frequencies

GnomAD3 genomes

AF:

0.233

AC:

35418

AN:

152074

Hom.:

5070

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0859

Gnomad AMI

AF:

0.396

Gnomad AMR

AF:

0.235

Gnomad ASJ

AF:

0.218

Gnomad EAS

AF:

0.00674

Gnomad SAS

AF:

0.188

Gnomad FIN

AF:

0.353

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.207

GnomAD2 exomes

AF:

0.243

AC:

60428

AN:

249112

AF XY:

0.247

show subpopulations

Gnomad AFR exome

AF:

0.0827

Gnomad AMR exome

AF:

0.182

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.00541

Gnomad FIN exome

AF:

0.345

Gnomad NFE exome

AF:

0.318

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.299

AC:

436065

AN:

1460232

Hom.:

69603

Cov.:

AF XY:

0.296

AC XY:

214925

AN XY:

726342

show subpopulations

African (AFR)

AF:

0.0754

AC:

2523

AN:

33464

American (AMR)

AF:

0.186

AC:

8284

AN:

44604

Ashkenazi Jewish (ASJ)

AF:

0.220

AC:

5753

AN:

26106

East Asian (EAS)

AF:

0.00343

AC:

136

AN:

39640

South Asian (SAS)

AF:

0.196

AC:

16914

AN:

86084

European-Finnish (FIN)

AF:

0.345

AC:

18381

AN:

53338

Middle Eastern (MID)

AF:

0.200

AC:

1142

AN:

5720

European-Non Finnish (NFE)

AF:

0.330

AC:

366580

AN:

1110920

Other (OTH)

AF:

0.271

AC:

16352

AN:

60356

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.476

Heterozygous variant carriers

14273

28545

42818

57090

71363

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.233

AC:

35417

AN:

152192

Hom.:

5067

Cov.:

AF XY:

0.233

AC XY:

17318

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0858

AC:

3564

AN:

41560

American (AMR)

AF:

0.235

AC:

3589

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.218

AC:

756

AN:

3470

East Asian (EAS)

AF:

0.00676

AC:

AN:

5178

South Asian (SAS)

AF:

0.188

AC:

907

AN:

4824

European-Finnish (FIN)

AF:

0.353

AC:

3728

AN:

10558

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.324

AC:

21996

AN:

67992

Other (OTH)

AF:

0.204

AC:

431

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1335

2670

4004

5339

6674

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.287

Hom.:

11282

Bravo

AF:

0.217

Asia WGS

AF:

0.109

AC:

380

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.31

(source)

DANN

Benign

0.39

PhyloP100

0.34

PromoterAI

-0.0012

Neutral

(source)

Mutation Taster

=99/1

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

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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22-50149702-C-T

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