3-39482025-C-T

Position:

• chr3-39482025-C-T

Variant summary

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

The NM_001393704.1(MOBP):​c.-5+1902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,038 control chromosomes in the GnomAD database, including 13,436 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 0.36 (13436 hom., cov: 32)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.61

Genes affected

MOBP (HGNC:7189): (myelin associated oligodendrocyte basic protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be a structural constituent of myelin sheath. Predicted to be involved in nervous system development. Predicted to be located in mitochondrion. Predicted to be active in cortical actin cytoskeleton. Implicated in frontotemporal dementia. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOBP	NM_001393704.1	c.-5+1902C>T		intron_variant		ENST00000684792.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOBP	ENST00000684792.1	c.-5+1902C>T		intron_variant			NM_001393704.1

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54068 AN: 151920 Hom.: 13395 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.356 AC: 54159 AN: 152038 Hom.: 13436 Cov.: 32 AF XY: 0.348 AC XY: 25901 AN XY: 74326

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.278

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.332

Alfa AF: 0.302 Hom.: 1680

Bravo AF: 0.376

Asia WGS AF: 0.336 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.77

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: rs1707956; hg19: chr3-39523516;