3-39494656-C-T

Position:

• chr3-39494656-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.-4-7410C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,820 control chromosomes in the GnomAD database, including 11,655 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 (11655 hom., cov: 31)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227

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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOBP	NM_001393704.1	c.-4-7410C>T		intron_variant		ENST00000684792.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOBP	ENST00000684792.1	c.-4-7410C>T		intron_variant			NM_001393704.1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58613 AN: 151702 Hom.: 11657 Cov.: 31

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.386 AC: 58630 AN: 151820 Hom.: 11655 Cov.: 31 AF XY: 0.386 AC XY: 28642 AN XY: 74212

Gnomad4 AFR AF: 0.342

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.367

Alfa AF: 0.399 Hom.: 15696

Bravo AF: 0.382

Asia WGS AF: 0.228 AC: 792 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.34

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: rs2370969; hg19: chr3-39536147;