chr7-2238591-C-T

Position:

• chr7-2238591-C-T

Variant summary

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

The NM_013393.3(MRM2):​c.298+827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,980 control chromosomes in the GnomAD database, including 8,813 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 (8808 hom., cov: 31)
  • Exomes 𝑓: 0.40 (5 hom.)
• Consequence: MRM2 NM_013393.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRM2	NM_013393.3	c.298+827G>A		intron_variant		ENST00000242257.14	NP_037525.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MRM2	ENST00000242257.14	c.298+827G>A		intron_variant		1	NM_013393.3	ENSP00000242257	P1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50918 AN: 151784 Hom.: 8805 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.347

GnomAD4 exome AF: 0.397 AC: 31 AN: 78 Hom.: 5 Cov.: 0 AF XY: 0.446 AC XY: 25 AN XY: 56

Gnomad4 AMR exome AF: 0.250

Gnomad4 FIN exome AF: 0.333

Gnomad4 NFE exome AF: 0.424

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.335 AC: 50934 AN: 151902 Hom.: 8808 Cov.: 31 AF XY: 0.335 AC XY: 24839 AN XY: 74214

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.257

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.345

Alfa AF: 0.354 Hom.: 18579

Bravo AF: 0.344

Asia WGS AF: 0.433 AC: 1504 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	3.0
DANN	Benign	0.70

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: rs7799006; hg19: chr7-2278226;