Genetic Variant MORN2:p.Asp70Asp (chr2-38880700-T-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_001145450.3(MORN2):c.210T>C(p.Asp70Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 1,549,902 control chromosomes in the GnomAD database, including 304 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 0.025 ( 83 hom., cov: 32)

Exomes 𝑓: 0.010 ( 221 hom. )

Consequence

MORN2
NM_001145450.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.841

Publications

11 publications found

Variant links:

Genes affected

MORN2 (HGNC:30166): (MORN repeat containing 2) Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

MORN2 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 (MetaRNN=0.0017122328).

BP7

Synonymous conserved (PhyloP=0.841 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MORN2	NM_001145450.3 link	c.210T>C	p.Asp70Asp	synonymous_variant	Exon 3 of 5	ENST00000644631.4	NP_001138922.2	Q502X0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORN2	ENST00000644631.4 link	c.210T>C	p.Asp70Asp	synonymous_variant	Exon 3 of 5		NM_001145450.3	ENSP00000494143.2		A0A2R8YE86

Frequencies

GnomAD3 genomes

AF:

0.0245

AC:

3729

AN:

152180

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0560

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.00576

Gnomad EAS

AF:

0.0693

Gnomad SAS

AF:

0.0209

Gnomad FIN

AF:

0.0186

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00728

Gnomad OTH

AF:

0.0210

GnomAD2 exomes

AF:

0.0170

AC:

2559

AN:

150862

AF XY:

0.0166

show subpopulations

Gnomad AFR exome

AF:

0.0527

Gnomad AMR exome

AF:

0.00829

Gnomad ASJ exome

AF:

0.00680

Gnomad EAS exome

AF:

0.0692

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.00786

Gnomad OTH exome

AF:

0.0184

GnomAD4 exome

AF:

0.0105

AC:

14653

AN:

1397604

Hom.:

221

Cov.:

AF XY:

0.0106

AC XY:

7331

AN XY:

689332

show subpopulations

African (AFR)

AF:

0.0582

AC:

1835

AN:

31548

American (AMR)

AF:

0.00884

AC:

315

AN:

35628

Ashkenazi Jewish (ASJ)

AF:

0.00691

AC:

174

AN:

25176

East Asian (EAS)

AF:

0.0586

AC:

2089

AN:

35658

South Asian (SAS)

AF:

0.0166

AC:

1312

AN:

79088

European-Finnish (FIN)

AF:

0.0169

AC:

813

AN:

48148

Middle Eastern (MID)

AF:

0.0418

AC:

238

AN:

5696

European-Non Finnish (NFE)

AF:

0.00639

AC:

6891

AN:

1078708

Other (OTH)

AF:

0.0170

AC:

986

AN:

57954

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.451

Heterozygous variant carriers

686

1372

2057

2743

3429

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.0246

AC:

3745

AN:

152298

Hom.:

Cov.:

AF XY:

0.0259

AC XY:

1932

AN XY:

74470

show subpopulations

African (AFR)

AF:

0.0562

AC:

2335

AN:

41566

American (AMR)

AF:

0.0117

AC:

179

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.00576

AC:

AN:

3470

East Asian (EAS)

AF:

0.0693

AC:

359

AN:

5182

South Asian (SAS)

AF:

0.0209

AC:

101

AN:

4832

European-Finnish (FIN)

AF:

0.0186

AC:

197

AN:

10608

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00728

AC:

495

AN:

68018

Other (OTH)

AF:

0.0227

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

177

355

532

710

887

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<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:

0.0135

Hom.:

117

Bravo

AF:

0.0258

TwinsUK

AF:

0.00485

AC:

ALSPAC

AF:

0.00804

AC:

ExAC

AF:

0.0167

AC:

316

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.20

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.40

CADD

Benign

7.6

(source)

DANN

Benign

0.87

Eigen

Benign

0.058

Eigen_PC

Benign

0.088

FATHMM_MKL

Benign

0.75

LIST_S2

Benign

0.33

MetaRNN

Benign

0.0017

MetaSVM

Benign

-1.0

PhyloP100

0.84

PROVEAN

Benign

0.36

REVEL

Benign

0.014

Sift

Pathogenic

0.0

Sift4G

Benign

0.29

Vest4

0.12

ClinPred

0.080

GERP RS

2.1

Mutation Taster

=289/11

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