chr3-39482025-C-T

Variant names:

• chr3-39482025-C-T
• rs1707956
• NM_001393704.1:c.-5+1902C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MOBP	NM_001393704.1	c.-5+1902C>T		intron_variant	Intron 2 of 3	ENST00000684792.1	NP_001380633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOBP	ENST00000684792.1	c.-5+1902C>T		intron_variant	Intron 2 of 3		NM_001393704.1	ENSP00000508923.1

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

African (AFR) AF: 0.708 AC: 29304 AN: 41416

American (AMR) AF: 0.228 AC: 3490 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 963 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1411 AN: 5174

South Asian (SAS) AF: 0.299 AC: 1441 AN: 4826

European-Finnish (FIN) AF: 0.168 AC: 1774 AN: 10584

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14817 AN: 67972

Other (OTH) AF: 0.332 AC: 701 AN: 2110

Alfa AF: 0.430 Hom.: 5107

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
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1707956; hg19: chr3-39523516;