Genetic Variant MOV10L1:c.282+37G>A (chr22-50092222-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.282+37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 1,575,500 control chromosomes in the GnomAD database, including 25,021 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 0.14 ( 1946 hom., cov: 32)

Exomes 𝑓: 0.18 ( 23075 hom. )

Consequence

MOV10L1
NM_018995.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.309

Publications

12 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018995.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MOV10L1	NM_018995.3	MANE Select	c.282+37G>A	intron	N/A	NP_061868.1
MOV10L1	NM_001164104.2		c.282+37G>A	intron	N/A	NP_001157576.1
MOV10L1	NM_001164105.2		c.222+37G>A	intron	N/A	NP_001157577.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MOV10L1	ENST00000262794.10	TSL:1 MANE Select	c.282+37G>A	intron	N/A	ENSP00000262794.5
MOV10L1	ENST00000395858.7	TSL:1	c.282+37G>A	intron	N/A	ENSP00000379199.3
MOV10L1	ENST00000395854.6	TSL:1	n.*438+37G>A	intron	N/A	ENSP00000379195.2

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22017

AN:

152026

Hom.:

1946

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0460

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.283

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.172

Gnomad OTH

AF:

0.159

GnomAD2 exomes

AF:

0.185

AC:

43496

AN:

235186

AF XY:

0.190

show subpopulations

Gnomad AFR exome

AF:

0.0404

Gnomad AMR exome

AF:

0.157

Gnomad ASJ exome

AF:

0.223

Gnomad EAS exome

AF:

0.268

Gnomad FIN exome

AF:

0.223

Gnomad NFE exome

AF:

0.178

Gnomad OTH exome

AF:

0.188

GnomAD4 exome

AF:

0.176

AC:

250290

AN:

1423356

Hom.:

23075

Cov.:

AF XY:

0.178

AC XY:

125771

AN XY:

706810

show subpopulations

African (AFR)

AF:

0.0428

AC:

1396

AN:

32638

American (AMR)

AF:

0.153

AC:

6490

AN:

42552

Ashkenazi Jewish (ASJ)

AF:

0.223

AC:

5503

AN:

24716

East Asian (EAS)

AF:

0.319

AC:

12554

AN:

39368

South Asian (SAS)

AF:

0.226

AC:

18595

AN:

82388

European-Finnish (FIN)

AF:

0.217

AC:

11413

AN:

52676

Middle Eastern (MID)

AF:

0.182

AC:

1020

AN:

5594

European-Non Finnish (NFE)

AF:

0.169

AC:

182881

AN:

1084456

Other (OTH)

AF:

0.177

AC:

10438

AN:

58968

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

10005

20010

30014

40019

50024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6500

13000

19500

26000

32500

<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:

0.145

AC:

22022

AN:

152144

Hom.:

1946

Cov.:

AF XY:

0.149

AC XY:

11106

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.0460

AC:

1910

AN:

41512

American (AMR)

AF:

0.145

AC:

2213

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.224

AC:

777

AN:

3470

East Asian (EAS)

AF:

0.283

AC:

1465

AN:

5180

South Asian (SAS)

AF:

0.229

AC:

1106

AN:

4820

European-Finnish (FIN)

AF:

0.221

AC:

2341

AN:

10570

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.172

AC:

11675

AN:

67982

Other (OTH)

AF:

0.158

AC:

334

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

952

1904

2855

3807

4759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.148

Hom.:

1073

Bravo

AF:

0.134

Asia WGS

AF:

0.253

AC:

878

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.58

(source)

DANN

Benign

0.67

PhyloP100

-0.31

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over