2-233809878-T-C

Variant names:

• chr2-233809878-T-C
• rs11674078
• NM_001394639.1:c.2448+600T>C

Variant summary

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

The NM_001394639.1(MROH2A):​c.2448+600T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 150,032 control chromosomes in the GnomAD database, including 2,668 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 0.18 (2668 hom., cov: 31)
• Consequence: MROH2A NM_001394639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.600
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MROH2A	NM_001394639.1	c.2448+600T>C		intron_variant	Intron 22 of 41	ENST00000389758.4	NP_001381568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MROH2A	ENST00000389758.4	c.2448+600T>C		intron_variant	Intron 22 of 41	5	NM_001394639.1	ENSP00000374408.3
MROH2A	ENST00000610772.4	c.2457+600T>C		intron_variant	Intron 22 of 41	5		ENSP00000477597.1

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27468 AN: 149910 Hom.: 2667 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.183 AC: 27472 AN: 150032 Hom.: 2668 Cov.: 31 AF XY: 0.180 AC XY: 13126 AN XY: 73116

African (AFR) AF: 0.149 AC: 6066 AN: 40616

American (AMR) AF: 0.138 AC: 2071 AN: 14998

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 848 AN: 3464

East Asian (EAS) AF: 0.205 AC: 1040 AN: 5062

South Asian (SAS) AF: 0.205 AC: 961 AN: 4688

European-Finnish (FIN) AF: 0.137 AC: 1402 AN: 10238

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14361 AN: 67690

Other (OTH) AF: 0.202 AC: 419 AN: 2074

Alfa AF: 0.206 Hom.: 6514

Bravo AF: 0.179

Asia WGS AF: 0.195 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.5
DANN	Benign	0.66
PhyloP100		0.60
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: rs11674078; hg19: chr2-234718524;