chr7-2236358-G-A

Position:

• chr7-2236358-G-A

Variant summary

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

The NM_013393.3(MRM2):​c.299-794C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,068 control chromosomes in the GnomAD database, including 8,864 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 0.34 (8864 hom., cov: 33)
• Consequence: MRM2 NM_013393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0930

Genes affected

MRM2 (HGNC:16352): (mitochondrial rRNA methyltransferase 2) The protein encoded by this gene is a member of the S-adenosylmethionine-binding protein family. It is a nucleolar protein and it may be involved in the processing and modification of rRNA. This gene has been suggested to be involved in cell cycle control and DNA repair. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRM2	NM_013393.3	c.299-794C>T		intron_variant		ENST00000242257.14	NP_037525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRM2	ENST00000242257.14	c.299-794C>T		intron_variant		1	NM_013393.3	ENSP00000242257	P1

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51058 AN: 151950 Hom.: 8862 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.336 AC: 51075 AN: 152068 Hom.: 8864 Cov.: 33 AF XY: 0.335 AC XY: 24931 AN XY: 74336

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.348

Alfa AF: 0.344 Hom.: 1419

Bravo AF: 0.345

Asia WGS AF: 0.434 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.81

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: rs7787274; hg19: chr7-2275993;