rs9784064

Positions:

• chr2-233777318-G-A

Variant summary

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

The ENST00000428446.5(MROH2A):​c.-13+1561G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0731 in 152,174 control chromosomes in the GnomAD database, including 1,106 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 0.073 (1106 hom., cov: 32)
• Consequence: MROH2A ENST00000428446.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH2A	NM_001367507.1	c.-15+1561G>A		intron_variant
MROH2A	XM_024452842.2	c.-15+1561G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH2A	ENST00000428446.5	c.-13+1561G>A		intron_variant		1
MROH2A	ENST00000430892.5	c.-15+1561G>A		intron_variant		1
MROH2A	ENST00000454283.1	c.-84+1561G>A		intron_variant		1
MROH2A	ENST00000610772.4	c.-15+1561G>A		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11120 AN: 152056 Hom.: 1104 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0289

Gnomad ASJ AF: 0.00864

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.0299

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0731 AC: 11131 AN: 152174 Hom.: 1106 Cov.: 32 AF XY: 0.0701 AC XY: 5218 AN XY: 74394

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.0288

Gnomad4 ASJ AF: 0.00864

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00808

Gnomad4 FIN AF: 0.0299

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0243 Hom.: 240

Bravo AF: 0.0804

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.73

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: rs9784064; hg19: chr2-234685964; COSMIC: COSV59397041; COSMIC: COSV59397041;