chr2-233783971-C-T

Variant names:

• chr2-233783971-C-T
• rs11690786
• NM_001394639.1:c.276+4119C>T

Variant summary

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

The NM_001367507.1(MROH2A):​c.276+4119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,582 control chromosomes in the GnomAD database, including 7,670 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 0.31 (7670 hom., cov: 32)
• Consequence: MROH2A NM_001367507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 6 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001367507.1. 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.276+4119C>T		intron	N/A	NP_001381568.1
	MROH2A	NM_001367507.1		c.276+4119C>T		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.276+4119C>T		intron	N/A	ENSP00000374408.3
	MROH2A	ENST00000610772.4	TSL:5	c.276+4119C>T		intron	N/A	ENSP00000477597.1
	MROH2A	ENST00000480634.2	TSL:5	n.182+4119C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47469 AN: 151464 Hom.: 7670 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.313 AC: 47496 AN: 151582 Hom.: 7670 Cov.: 32 AF XY: 0.318 AC XY: 23575 AN XY: 74080

African (AFR) AF: 0.326 AC: 13482 AN: 41302

American (AMR) AF: 0.275 AC: 4203 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1097 AN: 3464

East Asian (EAS) AF: 0.108 AC: 556 AN: 5170

South Asian (SAS) AF: 0.365 AC: 1758 AN: 4816

European-Finnish (FIN) AF: 0.405 AC: 4210 AN: 10406

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21164 AN: 67866

Other (OTH) AF: 0.285 AC: 599 AN: 2100

Alfa AF: 0.316 Hom.: 8505

Bravo AF: 0.304

Asia WGS AF: 0.220 AC: 763 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.11
PhyloP100		0.32
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: rs11690786; hg19: chr2-234692617;