dbSNP rs2272838: MOV10L1:p.Thr863Thr (chr22-50145772-A-C) – 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.2589A>C(p.Thr863Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,613,754 control chromosomes in the GnomAD database, including 50,202 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 ( 4319 hom., cov: 32)

Exomes 𝑓: 0.25 ( 45883 hom. )

Consequence

MOV10L1
NM_018995.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.72

Publications

18 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=-1.03).

BP7

Synonymous conserved (PhyloP=-2.72 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.2589A>C	p.Thr863Thr	synonymous_variant	Exon 19 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.2589A>C	p.Thr863Thr	synonymous_variant	Exon 19 of 27	1	NM_018995.3	ENSP00000262794.5	Q9BXT6-1
MOV10L1	ENST00000395858.7 link	c.2589A>C	p.Thr863Thr	synonymous_variant	Exon 19 of 26	1		ENSP00000379199.3	Q9BXT6-4
MOV10L1	ENST00000540615.5 link	c.2529A>C	p.Thr843Thr	synonymous_variant	Exon 19 of 26	2		ENSP00000438542.1	Q9BXT6-5

Frequencies

GnomAD3 genomes

AF:

0.227

AC:

34577

AN:

152018

Hom.:

4304

Cov.:

show subpopulations

Gnomad AFR

AF:

0.157

Gnomad AMI

AF:

0.241

Gnomad AMR

AF:

0.353

Gnomad ASJ

AF:

0.260

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.317

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.269

GnomAD2 exomes

AF:

0.269

AC:

67691

AN:

251378

AF XY:

0.270

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.413

Gnomad ASJ exome

AF:

0.252

Gnomad EAS exome

AF:

0.278

Gnomad FIN exome

AF:

0.201

Gnomad NFE exome

AF:

0.240

Gnomad OTH exome

AF:

0.273

GnomAD4 exome

AF:

0.247

AC:

360747

AN:

1461616

Hom.:

45883

Cov.:

AF XY:

0.249

AC XY:

181094

AN XY:

727102

show subpopulations

African (AFR)

AF:

0.160

AC:

5362

AN:

33476

American (AMR)

AF:

0.411

AC:

18385

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

6433

AN:

26136

East Asian (EAS)

AF:

0.283

AC:

11251

AN:

39696

South Asian (SAS)

AF:

0.320

AC:

27578

AN:

86254

European-Finnish (FIN)

AF:

0.202

AC:

10786

AN:

53324

Middle Eastern (MID)

AF:

0.256

AC:

1473

AN:

5746

European-Non Finnish (NFE)

AF:

0.238

AC:

264442

AN:

1111882

Other (OTH)

AF:

0.249

AC:

15037

AN:

60384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

15401

30801

46202

61602

77003

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9198

18396

27594

36792

45990

<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:

0.228

AC:

34621

AN:

152138

Hom.:

4319

Cov.:

AF XY:

0.229

AC XY:

16995

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.157

AC:

6509

AN:

41494

American (AMR)

AF:

0.354

AC:

5409

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.260

AC:

902

AN:

3472

East Asian (EAS)

AF:

0.271

AC:

1399

AN:

5170

South Asian (SAS)

AF:

0.317

AC:

1532

AN:

4826

European-Finnish (FIN)

AF:

0.189

AC:

1996

AN:

10582

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.235

AC:

16011

AN:

67996

Other (OTH)

AF:

0.276

AC:

584

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1390

2780

4169

5559

6949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

366

732

1098

1464

1830

<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:

0.239

Hom.:

7208

Bravo

AF:

0.239

Asia WGS

AF:

0.304

AC:

1057

AN:

3478

EpiCase

AF:

0.231

EpiControl

AF:

0.236

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.0080

(source)

DANN

Benign

0.28

PhyloP100

-2.7

Mutation Taster

=283/17

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