2-233794419-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_001394639.1(MROH2A):c.879C>T(p.Asn293=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00633 in 1,550,478 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0047 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0065 (40 hom.)
• Consequence: MROH2A NM_001394639.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.716

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 -11 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BP6: Variant 2-233794419-C-T is Benign according to our data. Variant chr2-233794419-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2652024.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.716 with no splicing effect.
• BS2: High Homozygotes in GnomAd at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MROH2A	NM_001394639.1	c.879C>T	p.Asn293=	synonymous_variant	8/42	ENST00000389758.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MROH2A	ENST00000389758.4	c.879C>T	p.Asn293=	synonymous_variant	8/42	5	NM_001394639.1	A2
MROH2A	ENST00000610772.4	c.879C>T	p.Asn293=	synonymous_variant	8/42	5		P4

Frequencies

GnomAD3 genomes AF: 0.00475 AC: 723 AN: 152102 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00145

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.00917

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00660

Gnomad OTH AF: 0.00671

GnomAD3 exomes AF: 0.00403 AC: 591 AN: 146764 Hom.: 1 AF XY: 0.00395 AC XY: 313 AN XY: 79156

Gnomad AFR exome AF: 0.00103

Gnomad AMR exome AF: 0.00497

Gnomad ASJ exome AF: 0.00681

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000532

Gnomad FIN exome AF: 0.00111

Gnomad NFE exome AF: 0.00640

Gnomad OTH exome AF: 0.00680

GnomAD4 exome AF: 0.00650 AC: 9088 AN: 1398258 Hom.: 40 Cov.: 32 AF XY: 0.00634 AC XY: 4369 AN XY: 689656

Gnomad4 AFR exome AF: 0.00133

Gnomad4 AMR exome AF: 0.00527

Gnomad4 ASJ exome AF: 0.00596

Gnomad4 EAS exome AF: 0.000224

Gnomad4 SAS exome AF: 0.000606

Gnomad4 FIN exome AF: 0.00139

Gnomad4 NFE exome AF: 0.00764

Gnomad4 OTH exome AF: 0.00593

GnomAD4 genome AF: 0.00475 AC: 723 AN: 152220 Hom.: 3 Cov.: 32 AF XY: 0.00462 AC XY: 344 AN XY: 74422

Gnomad4 AFR AF: 0.00144

Gnomad4 AMR AF: 0.00916

Gnomad4 ASJ AF: 0.00576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00123

Gnomad4 NFE AF: 0.00660

Gnomad4 OTH AF: 0.00664

Alfa AF: 0.00527 Hom.: 0

Bravo AF: 0.00566

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Nov 01, 2022

MROH2A: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	0.47
Dann	Benign	0.64

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs187531871; hg19: chr2-234703065;