rs2361502

Positions:

• chr2-233790144-T-C

Variant summary

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

The NM_001394639.1(MROH2A):​c.571+130T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 918,056 control chromosomes in the GnomAD database, including 40,448 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 0.30 (6943 hom., cov: 31)
  • Exomes 𝑓: 0.29 (33505 hom.)
• Consequence: MROH2A NM_001394639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

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]

MROH2A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MROH2A	NM_001394639.1	c.571+130T>C		intron_variant		ENST00000389758.4	NP_001381568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MROH2A	ENST00000389758.4	c.571+130T>C		intron_variant		5	NM_001394639.1	ENSP00000374408.3
MROH2A	ENST00000610772.4	c.571+130T>C		intron_variant		5		ENSP00000477597.1
MROH2A	ENST00000480634.2	n.183-3529T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45449 AN: 151816 Hom.: 6940 Cov.: 31

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.276

GnomAD4 exome AF: 0.291 AC: 222991 AN: 766122 Hom.: 33505 AF XY: 0.293 AC XY: 112162 AN XY: 382606

Gnomad4 AFR exome AF: 0.339

Gnomad4 AMR exome AF: 0.287

Gnomad4 ASJ exome AF: 0.321

Gnomad4 EAS exome AF: 0.108

Gnomad4 SAS exome AF: 0.372

Gnomad4 FIN exome AF: 0.301

Gnomad4 NFE exome AF: 0.292

Gnomad4 OTH exome AF: 0.288

GnomAD4 genome AF: 0.299 AC: 45478 AN: 151934 Hom.: 6943 Cov.: 31 AF XY: 0.301 AC XY: 22380 AN XY: 74270

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.273

Alfa AF: 0.295 Hom.: 14358

Bravo AF: 0.298

Asia WGS AF: 0.232 AC: 805 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.43
DANN	Benign	0.64

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

Other links and lift over

dbSNP: rs2361502; hg19: chr2-234698790; COSMIC: COSV67681126;