dbSNP rs2272840: MOV10L1:c.2727+10G>A (chr22-50149724-G-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.2727+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 1,608,630 control chromosomes in the GnomAD database, including 50,022 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 ( 4350 hom., cov: 32)

Exomes 𝑓: 0.25 ( 45672 hom. )

Consequence

MOV10L1
NM_018995.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.356

Publications

9 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:

Genome browser will be placed here

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=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.2727+10G>A		intron_variant	Intron 20 of 26	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.2727+10G>A		intron_variant	Intron 20 of 26	1	NM_018995.3	ENSP00000262794.5		Q9BXT6-1

Frequencies

GnomAD3 genomes

AF:

0.229

AC:

34758

AN:

151988

Hom.:

4335

Cov.:

show subpopulations

Gnomad AFR

AF:

0.160

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.356

Gnomad ASJ

AF:

0.263

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.318

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.235

Gnomad OTH

AF:

0.272

GnomAD2 exomes

AF:

0.271

AC:

66337

AN:

245022

AF XY:

0.272

show subpopulations

Gnomad AFR exome

AF:

0.161

Gnomad AMR exome

AF:

0.409

Gnomad ASJ exome

AF:

0.254

Gnomad EAS exome

AF:

0.273

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.241

Gnomad OTH exome

AF:

0.276

GnomAD4 exome

AF:

0.247

AC:

359802

AN:

1456524

Hom.:

45672

Cov.:

AF XY:

0.249

AC XY:

180674

AN XY:

724446

show subpopulations

African (AFR)

AF:

0.163

AC:

5439

AN:

33394

American (AMR)

AF:

0.409

AC:

18058

AN:

44192

Ashkenazi Jewish (ASJ)

AF:

0.248

AC:

6457

AN:

26026

East Asian (EAS)

AF:

0.281

AC:

11127

AN:

39604

South Asian (SAS)

AF:

0.323

AC:

27673

AN:

85742

European-Finnish (FIN)

AF:

0.209

AC:

11105

AN:

53190

Middle Eastern (MID)

AF:

0.260

AC:

1453

AN:

5584

European-Non Finnish (NFE)

AF:

0.238

AC:

263410

AN:

1108598

Other (OTH)

AF:

0.251

AC:

15080

AN:

60194

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

14080

28160

42240

56320

70400

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9158

18316

27474

36632

45790

<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:

0.229

AC:

34802

AN:

152106

Hom.:

4350

Cov.:

AF XY:

0.230

AC XY:

17133

AN XY:

74380

show subpopulations

African (AFR)

AF:

0.159

AC:

6612

AN:

41500

American (AMR)

AF:

0.356

AC:

5448

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.263

AC:

914

AN:

3470

East Asian (EAS)

AF:

0.268

AC:

1387

AN:

5170

South Asian (SAS)

AF:

0.319

AC:

1534

AN:

4812

European-Finnish (FIN)

AF:

0.195

AC:

2065

AN:

10584

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.235

AC:

15987

AN:

67964

Other (OTH)

AF:

0.279

AC:

589

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1361

2722

4083

5444

6805

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

368

736

1104

1472

1840

<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:

0.223

Hom.:

1212

Bravo

AF:

0.239

Asia WGS

AF:

0.307

AC:

1065

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.1

(source)

DANN

Benign

0.32

PhyloP100

-0.36

PromoterAI

0.015

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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