rs3099950

Variant names:

• chr2-38882417-G-A
• rs3099950
• NM_001145450.3:c.358G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 36 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MORN2	NM_001145450.3	c.358G>A	p.Glu120Lys	missense_variant	Exon 5 of 5	ENST00000644631.4	NP_001138922.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MORN2	ENST00000644631.4	c.358G>A	p.Glu120Lys	missense_variant	Exon 5 of 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

GnomAD2 exomes AF: 0.108 AC: 17144 AN: 158612 AF XY: 0.114

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 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

African (AFR) AF: 0.0167 AC: 527 AN: 31468

American (AMR) AF: 0.103 AC: 3639 AN: 35502

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 2460 AN: 24970

East Asian (EAS) AF: 0.000422 AC: 15 AN: 35548

South Asian (SAS) AF: 0.158 AC: 12361 AN: 78336

European-Finnish (FIN) AF: 0.132 AC: 6464 AN: 49066

Middle Eastern (MID) AF: 0.0951 AC: 540 AN: 5680

European-Non Finnish (NFE) AF: 0.122 AC: 130090 AN: 1068680

Other (OTH) AF: 0.104 AC: 5997 AN: 57550

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

African (AFR) AF: 0.0227 AC: 943 AN: 41508

American (AMR) AF: 0.105 AC: 1605 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3468

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5186

South Asian (SAS) AF: 0.151 AC: 727 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1454 AN: 10546

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8301 AN: 67968

Other (OTH) AF: 0.0891 AC: 188 AN: 2110

Alfa AF: 0.110 Hom.: 2555

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
PhyloP100		6.2
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
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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