2-233817173-A-G

Variant names:

• chr2-233817173-A-G
• rs726017
• NM_001394639.1:c.2961+288A>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.2961+288A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,200 control chromosomes in the GnomAD database, including 53,573 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 0.84 (53573 hom., cov: 32)
• Consequence: MROH2A NM_001394639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MROH2A	NM_001394639.1	c.2961+288A>G		intron_variant	Intron 27 of 41	ENST00000389758.4	NP_001381568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MROH2A	ENST00000389758.4	c.2961+288A>G		intron_variant	Intron 27 of 41	5	NM_001394639.1	ENSP00000374408.3
MROH2A	ENST00000610772.4	c.2970+288A>G		intron_variant	Intron 27 of 41	5		ENSP00000477597.1

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127507 AN: 152082 Hom.: 53509 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.815

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.839 AC: 127634 AN: 152200 Hom.: 53573 Cov.: 32 AF XY: 0.841 AC XY: 62605 AN XY: 74422

African (AFR) AF: 0.820 AC: 34011 AN: 41490

American (AMR) AF: 0.815 AC: 12473 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.863 AC: 2996 AN: 3470

East Asian (EAS) AF: 0.894 AC: 4632 AN: 5184

South Asian (SAS) AF: 0.855 AC: 4127 AN: 4826

European-Finnish (FIN) AF: 0.890 AC: 9449 AN: 10618

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57145 AN: 68000

Other (OTH) AF: 0.851 AC: 1794 AN: 2108

Alfa AF: 0.843 Hom.: 27348

Bravo AF: 0.834

Asia WGS AF: 0.886 AC: 3080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.4
DANN	Benign	0.58
PhyloP100		0.26
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: rs726017; hg19: chr2-234725819;