Genetic Variant MOV10L1:n.-22_-21insGGTG (chr22-50090067-C-CGGTG) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_018995.3(MOV10L1):c.-22_-21insGGTG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 1,237,866 control chromosomes in the GnomAD database, including 32,883 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.22 ( 4029 hom., cov: 33)

Exomes 𝑓: 0.23 ( 28854 hom. )

Consequence

MOV10L1
NM_018995.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.91

Publications

0 publications found

Variant links:

COSMIC-nc: COSV104585081

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 -10 ACMG points.

BP6

Variant 22-50090067-C-CGGTG is Benign according to our data. Variant chr22-50090067-C-CGGTG is described in ClinVar as [Likely_benign]. Clinvar id is 3911534.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOV10L1	NM_018995.3 link	c.-22_-21insGGTG		5_prime_UTR_variant	Exon 1 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.-22_-21insGGTG		5_prime_UTR_variant	Exon 1 of 27	1	NM_018995.3	ENSP00000262794.5		Q9BXT6-1

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33294

AN:

151130

Hom.:

4015

Cov.:

show subpopulations

Gnomad AFR

AF:

0.153

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.252

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.314

Gnomad FIN

AF:

0.170

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.228

Gnomad OTH

AF:

0.259

GnomAD2 exomes

AF:

0.0225

AC:

119

AN:

5282

AF XY:

0.0255

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0132

Gnomad NFE exome

AF:

0.0927

Gnomad OTH exome

AF:

0.0556

GnomAD4 exome

AF:

0.227

AC:

246322

AN:

1086630

Hom.:

28854

Cov.:

AF XY:

0.227

AC XY:

117016

AN XY:

515674

show subpopulations

African (AFR)

AF:

0.152

AC:

3388

AN:

22262

American (AMR)

AF:

0.372

AC:

2870

AN:

7718

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

3107

AN:

13612

East Asian (EAS)

AF:

0.271

AC:

6792

AN:

25028

South Asian (SAS)

AF:

0.303

AC:

6939

AN:

22922

European-Finnish (FIN)

AF:

0.161

AC:

4830

AN:

29978

Middle Eastern (MID)

AF:

0.223

AC:

700

AN:

3144

European-Non Finnish (NFE)

AF:

0.226

AC:

207805

AN:

918966

Other (OTH)

AF:

0.230

AC:

9891

AN:

43000

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.407

Heterozygous variant carriers

9747

19494

29242

38989

48736

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.220

AC:

33332

AN:

151236

Hom.:

4029

Cov.:

AF XY:

0.221

AC XY:

16330

AN XY:

73868

show subpopulations

African (AFR)

AF:

0.153

AC:

6350

AN:

41486

American (AMR)

AF:

0.346

AC:

5234

AN:

15124

Ashkenazi Jewish (ASJ)

AF:

0.252

AC:

871

AN:

3454

East Asian (EAS)

AF:

0.267

AC:

1375

AN:

5154

South Asian (SAS)

AF:

0.315

AC:

1520

AN:

4830

European-Finnish (FIN)

AF:

0.170

AC:

1747

AN:

10280

Middle Eastern (MID)

AF:

0.195

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.228

AC:

15399

AN:

67606

Other (OTH)

AF:

0.266

AC:

558

AN:

2098

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1341

2683

4024

5366

6707

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0625

Hom.:

112

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Feb 16, 2025

Laboratory of Genetics, Children's Clinical University Hospital Latvia

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

-1.9

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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chr22-50090067-C-CGGTG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over