rs4240897

chr1-11982698-G-Achr1-11982698-G-T

Variant summary

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

The NM_014874.4(MFN2):c.-5+584G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,950 control chromosomes in the GnomAD database, including 14,402 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 0.43 (14402 hom., cov: 32)
  • Exomes 𝑓: 0.38 (0 hom.)
• Consequence: MFN2 NM_014874.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

Genes affected

MFN2 (HGNC:16877): (mitofusin 2) This gene encodes a mitochondrial membrane protein that participates in mitochondrial fusion and contributes to the maintenance and operation of the mitochondrial network. This protein is involved in the regulation of vascular smooth muscle cell proliferation, and it may play a role in the pathophysiology of obesity. Mutations in this gene cause Charcot-Marie-Tooth disease type 2A2, and hereditary motor and sensory neuropathy VI, which are both disorders of the peripheral nervous system. Defects in this gene have also been associated with early-onset stroke. Two transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MFN2	NM_014874.4	c.-5+584G>A		intron_variant		ENST00000235329.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MFN2	ENST00000235329.10	c.-5+584G>A		intron_variant		1	NM_014874.4	P1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65130 AN: 151824 Hom.: 14396 Cov.: 32

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.409

GnomAD4 exome AF: 0.375 AC: 3 AN: 8 Hom.: 0 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.429 AC: 65167 AN: 151942 Hom.: 14402 Cov.: 32 AF XY: 0.436 AC XY: 32371 AN XY: 74256

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.554

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.411

Alfa AF: 0.408 Hom.: 12959

Bravo AF: 0.410

Asia WGS AF: 0.548 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	11
Dann	Benign	0.83

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: rs4240897; hg19: chr1-12042755;