chr3-39485383-C-T

Variant names:

• chr3-39485383-C-T
• rs1464047
• NM_001393704.1:c.-5+5260C>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+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
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393704.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOBP	NM_001393704.1	MANE Select	c.-5+5260C>T		intron	N/A	NP_001380633.1	Q13875-1
	MOBP	NM_001278322.2		c.-5+5260C>T		intron	N/A	NP_001265251.1	Q13875-4
	MOBP	NM_001278323.2		c.-4-16683C>T		intron	N/A	NP_001265252.1	Q13875-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOBP	ENST00000684792.1	MANE Select	c.-5+5260C>T		intron	N/A	ENSP00000508923.1	Q13875-1
	MOBP	ENST00000383754.7	TSL:1	c.-5+5260C>T		intron	N/A	ENSP00000373261.3	Q13875-3
	MOBP	ENST00000452959.6	TSL:1	n.-5+5260C>T		intron	N/A	ENSP00000405549.1	Q13875-3

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

African (AFR) AF: 0.203 AC: 8401 AN: 41456

American (AMR) AF: 0.384 AC: 5871 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1477 AN: 3472

East Asian (EAS) AF: 0.124 AC: 638 AN: 5162

South Asian (SAS) AF: 0.361 AC: 1740 AN: 4818

European-Finnish (FIN) AF: 0.484 AC: 5107 AN: 10554

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 34013 AN: 67968

Other (OTH) AF: 0.380 AC: 802 AN: 2110

Alfa AF: 0.462 Hom.: 30672

Bravo AF: 0.366

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.0
DANN	Benign	0.72
PhyloP100		-0.25
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: rs1464047; hg19: chr3-39526874;