3-39481512-T-C

Position:

• chr3-39481512-T-C

Variant summary

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

The NM_001393704.1(MOBP):​c.-5+1389T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,102 control chromosomes in the GnomAD database, including 44,844 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 0.76 (44844 hom., cov: 31)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOBP	NM_001393704.1	c.-5+1389T>C		intron_variant		ENST00000684792.1	NP_001380633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOBP	ENST00000684792.1	c.-5+1389T>C		intron_variant			NM_001393704.1	ENSP00000508923

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114809 AN: 151984 Hom.: 44785 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.756 AC: 114918 AN: 152102 Hom.: 44844 Cov.: 31 AF XY: 0.746 AC XY: 55466 AN XY: 74350

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.704

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.729

Alfa AF: 0.712 Hom.: 58791

Bravo AF: 0.756

Asia WGS AF: 0.555 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.69

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: rs1768208; hg19: chr3-39523003;