chr2-233817718-A-T

Position:

• chr2-233817718-A-T

Variant summary

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

The NM_001394639.1(MROH2A):​c.2962-284A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,228 control chromosomes in the GnomAD database, including 1,841 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 0.13 (1841 hom., cov: 33)
• Consequence: MROH2A NM_001394639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MROH2A	NM_001394639.1	c.2962-284A>T		intron_variant		ENST00000389758.4	NP_001381568.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MROH2A	ENST00000389758.4	c.2962-284A>T		intron_variant		5	NM_001394639.1	ENSP00000374408	A2
MROH2A	ENST00000610772.4	c.2971-284A>T		intron_variant		5		ENSP00000477597	P4

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20400 AN: 152110 Hom.: 1831 Cov.: 33

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.0507

Gnomad FIN AF: 0.0787

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.134 AC: 20430 AN: 152228 Hom.: 1841 Cov.: 33 AF XY: 0.133 AC XY: 9920 AN XY: 74450

Gnomad4 AFR AF: 0.233

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.0506

Gnomad4 FIN AF: 0.0787

Gnomad4 NFE AF: 0.0785

Gnomad4 OTH AF: 0.126

Alfa AF: 0.108 Hom.: 134

Bravo AF: 0.147

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs6752792; hg19: chr2-234726364;