chr2-38882417-G-A

Position:

• chr2-38882417-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001145450.3(MORN2):​c.358G>A​(p.Glu120Lys) variant causes a missense change. The variant allele was found at a frequency of 0.114 in 1,538,888 control chromosomes in the GnomAD database, including 11,090 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 0.090 (811 hom., cov: 31)
  • Exomes 𝑓: 0.12 (10279 hom.)
• Consequence: MORN2 NM_001145450.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.19

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.002063483).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MORN2	NM_001145450.3	c.358G>A	p.Glu120Lys	missense_variant	5/5	ENST00000644631.4	NP_001138922.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MORN2	ENST00000644631.4	c.358G>A	p.Glu120Lys	missense_variant	5/5		NM_001145450.3	ENSP00000494143.2

Frequencies

GnomAD3 genomes AF: 0.0901 AC: 13700 AN: 151970 Hom.: 809 Cov.: 31

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.00192

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0905

GnomAD3 exomes AF: 0.108 AC: 17144 AN: 158612 Hom.: 1102 AF XY: 0.114 AC XY: 9460 AN XY: 83332

Gnomad AFR exome AF: 0.0174

Gnomad AMR exome AF: 0.102

Gnomad ASJ exome AF: 0.0952

Gnomad EAS exome AF: 0.000355

Gnomad SAS exome AF: 0.160

Gnomad FIN exome AF: 0.135

Gnomad NFE exome AF: 0.119

Gnomad OTH exome AF: 0.101

GnomAD4 exome AF: 0.117 AC: 162093 AN: 1386800 Hom.: 10279 Cov.: 27 AF XY: 0.119 AC XY: 81212 AN XY: 684428

Gnomad4 AFR exome AF: 0.0167

Gnomad4 AMR exome AF: 0.103

Gnomad4 ASJ exome AF: 0.0985

Gnomad4 EAS exome AF: 0.000422

Gnomad4 SAS exome AF: 0.158

Gnomad4 FIN exome AF: 0.132

Gnomad4 NFE exome AF: 0.122

Gnomad4 OTH exome AF: 0.104

GnomAD4 genome AF: 0.0900 AC: 13695 AN: 152088 Hom.: 811 Cov.: 31 AF XY: 0.0909 AC XY: 6759 AN XY: 74350

Gnomad4 AFR AF: 0.0227

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0891

Alfa AF: 0.114 Hom.: 1960

Bravo AF: 0.0812

TwinsUK AF: 0.125 AC: 463

ALSPAC AF: 0.119 AC: 457

ESP6500AA AF: 0.0260 AC: 36

ESP6500EA AF: 0.117 AC: 373

ExAC AF: 0.112 AC: 2880

Asia WGS AF: 0.0710 AC: 250 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.36
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.10
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.011	T;T;T;.;.;.
Eigen	Pathogenic	0.69
Eigen_PC	Pathogenic	0.68
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.90	D;.;.;D;D;D
MetaRNN	Benign	0.0021	T;T;T;T;T;T
MetaSVM	Benign	-0.80	T
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-2.1	N;N;N;D;.;N
REVEL	Benign	0.15
Sift	Benign	0.077	T;T;T;D;.;D
Sift4G	Benign	0.13	T;T;T;D;.;T
Polyphen		1.0	D;D;D;.;.;.
Vest4		0.26
ClinPred		0.015	T
GERP RS		5.4
Varity_R		0.53
gMVP		0.51

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

LitVar

Other links and lift over

dbSNP: rs3099950; hg19: chr2-39109558; COSMIC: COSV61320884; COSMIC: COSV61320884;