3-39485383-C-T

Position:

• chr3-39485383-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+5260C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,026 control chromosomes in the GnomAD database, including 12,796 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 0.39 (12796 hom., cov: 32)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOBP	NM_001393704.1	c.-5+5260C>T		intron_variant		ENST00000684792.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOBP	ENST00000684792.1	c.-5+5260C>T		intron_variant			NM_001393704.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58525 AN: 151908 Hom.: 12795 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.385 AC: 58531 AN: 152026 Hom.: 12796 Cov.: 32 AF XY: 0.383 AC XY: 28418 AN XY: 74278

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.380

Alfa AF: 0.471 Hom.: 25528

Bravo AF: 0.366

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.72

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: rs1464047; hg19: chr3-39526874;