Genetic Variant NM_001145450.3:c.210T>C (chr2-38880700-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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

GnomAD3 exomes

AF:

0.0170

AC:

2559

AN:

150862

Hom.:

AF XY:

0.0166

AC XY:

1343

AN XY:

81108

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 SAS exome

AF:

0.0165

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

Gnomad4 AFR exome

AF:

0.0582

Gnomad4 AMR exome

AF:

0.00884

Gnomad4 ASJ exome

AF:

0.00691

Gnomad4 EAS exome

AF:

0.0586

Gnomad4 SAS exome

AF:

0.0166

Gnomad4 FIN exome

AF:

0.0169

Gnomad4 NFE exome

AF:

0.00639

Gnomad4 OTH exome

AF:

0.0170

GnomAD4 genome

AF:

0.0246

AC:

3745

AN:

152298

Hom.:

Cov.:

AF XY:

0.0259

AC XY:

1932

AN XY:

74470

show subpopulations

Gnomad4 AFR

AF:

0.0562

Gnomad4 AMR

AF:

0.0117

Gnomad4 ASJ

AF:

0.00576

Gnomad4 EAS

AF:

0.0693

Gnomad4 SAS

AF:

0.0209

Gnomad4 FIN

AF:

0.0186

Gnomad4 NFE

AF:

0.00728

Gnomad4 OTH

AF:

0.0227

Alfa

AF:

0.0114

Hom.:

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

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.40

CADD

Benign

7.6

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

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

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over