3-39494656-C-T

Variant names:

• chr3-39494656-C-T
• rs2370969
• NM_001393704.1:c.-4-7410C>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.-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
• 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]

ENSG00000285885 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.-4-7410C>T		intron	N/A	NP_001380633.1	Q13875-1
	MOBP	NM_001278322.2		c.-4-7410C>T		intron	N/A	NP_001265251.1	Q13875-4
	MOBP	NM_001278323.2		c.-4-7410C>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.-4-7410C>T		intron	N/A	ENSP00000508923.1	Q13875-1
	MOBP	ENST00000383754.7	TSL:1	c.-4-7410C>T		intron	N/A	ENSP00000373261.3	Q13875-3
	MOBP	ENST00000452959.6	TSL:1	n.-4-7410C>T		intron	N/A	ENSP00000405549.1	Q13875-3

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

African (AFR) AF: 0.342 AC: 14157 AN: 41342

American (AMR) AF: 0.423 AC: 6450 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1269 AN: 3464

East Asian (EAS) AF: 0.156 AC: 810 AN: 5176

South Asian (SAS) AF: 0.299 AC: 1439 AN: 4814

European-Finnish (FIN) AF: 0.420 AC: 4410 AN: 10508

Middle Eastern (MID) AF: 0.252 AC: 73 AN: 290

European-Non Finnish (NFE) AF: 0.424 AC: 28810 AN: 67942

Other (OTH) AF: 0.367 AC: 773 AN: 2106

Alfa AF: 0.397 Hom.: 21621

Bravo AF: 0.382

Asia WGS AF: 0.228 AC: 792 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.2
DANN	Benign	0.34
PhyloP100		-0.23
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: rs2370969; hg19: chr3-39536147;