chr2-233797521-A-G

Variant names:

• chr2-233797521-A-G
• rs741159
• NM_001394639.1:c.1252+1208A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001394639.1(MROH2A):​c.1252+1208A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,130 control chromosomes in the GnomAD database, including 50,997 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 0.82 (50997 hom., cov: 32)
• Consequence: MROH2A NM_001394639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 3 publications found

Genes affected

MROH2A (HGNC:27936): (maestro heat like repeat family member 2A) This gene encodes a HEAT-domain-containing protein. The function of the encoded protein has not been characterized. [provided by RefSeq, Aug 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394639.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH2A	NM_001394639.1	MANE Select	c.1252+1208A>G		intron	N/A	NP_001381568.1	A6NES4
	MROH2A	NM_001367507.1		c.1252+1208A>G		intron	N/A	NP_001354436.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MROH2A	ENST00000389758.4	TSL:5 MANE Select	c.1252+1208A>G		intron	N/A	ENSP00000374408.3	A6NES4
	MROH2A	ENST00000610772.4	TSL:5	c.1261+1208A>G		intron	N/A	ENSP00000477597.1	A0A087WT58
	MROH2A	ENST00000477506.2	TSL:3	n.26+1208A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124143 AN: 152012 Hom.: 50972 Cov.: 32

Gnomad AFR AF: 0.745

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.755

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.785

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.864

Gnomad OTH AF: 0.819

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.817 AC: 124226 AN: 152130 Hom.: 50997 Cov.: 32 AF XY: 0.818 AC XY: 60838 AN XY: 74382

African (AFR) AF: 0.745 AC: 30881 AN: 41462

American (AMR) AF: 0.754 AC: 11531 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2723 AN: 3472

East Asian (EAS) AF: 0.785 AC: 4059 AN: 5172

South Asian (SAS) AF: 0.856 AC: 4132 AN: 4826

European-Finnish (FIN) AF: 0.891 AC: 9443 AN: 10598

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.864 AC: 58729 AN: 68002

Other (OTH) AF: 0.819 AC: 1724 AN: 2106

Alfa AF: 0.847 Hom.: 26370

Bravo AF: 0.804

Asia WGS AF: 0.801 AC: 2784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.23
PhyloP100		0.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs741159; hg19: chr2-234706167;