chr3-39513295-C-T

Variant names:

• chr3-39513295-C-T
• rs2233204
• ENST00000383754.7:c.207-88C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001278322.2(MOBP):​c.621-88C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,247,652 control chromosomes in the GnomAD database, including 70,728 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 0.26 (6200 hom., cov: 33)
  • Exomes 𝑓: 0.34 (64528 hom.)
• Consequence: MOBP NM_001278322.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001278322.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOBP	NM_001278322.2		c.621-88C>T		intron	N/A	NP_001265251.1
	MOBP	NM_182935.4		c.207-88C>T		intron	N/A	NP_891980.1
	MOBP	NR_003090.3		n.356-88C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOBP	ENST00000383754.7	TSL:1	c.207-88C>T		intron	N/A	ENSP00000373261.3
	MOBP	ENST00000424090.5	TSL:1	n.*35-88C>T		intron	N/A	ENSP00000389055.1
	MOBP	ENST00000442631.5	TSL:1	n.549-88C>T		intron	N/A	ENSP00000413771.1

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39060 AN: 152010 Hom.: 6200 Cov.: 33

Gnomad AFR AF: 0.0920

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0824

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.252

GnomAD4 exome AF: 0.335 AC: 367401 AN: 1095524 Hom.: 64528 AF XY: 0.335 AC XY: 185781 AN XY: 555094

African (AFR) AF: 0.0847 AC: 2084 AN: 24612

American (AMR) AF: 0.180 AC: 5948 AN: 33030

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 6510 AN: 21250

East Asian (EAS) AF: 0.112 AC: 3992 AN: 35752

South Asian (SAS) AF: 0.266 AC: 18185 AN: 68312

European-Finnish (FIN) AF: 0.374 AC: 18048 AN: 48212

Middle Eastern (MID) AF: 0.256 AC: 1270 AN: 4970

European-Non Finnish (NFE) AF: 0.366 AC: 296910 AN: 811794

Other (OTH) AF: 0.304 AC: 14454 AN: 47592

GnomAD4 genome AF: 0.257 AC: 39048 AN: 152128 Hom.: 6200 Cov.: 33 AF XY: 0.258 AC XY: 19151 AN XY: 74360

African (AFR) AF: 0.0917 AC: 3809 AN: 41524

American (AMR) AF: 0.228 AC: 3488 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3468

East Asian (EAS) AF: 0.0832 AC: 431 AN: 5182

South Asian (SAS) AF: 0.253 AC: 1222 AN: 4822

European-Finnish (FIN) AF: 0.378 AC: 3982 AN: 10542

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24174 AN: 67988

Other (OTH) AF: 0.249 AC: 526 AN: 2114

Alfa AF: 0.319 Hom.: 19468

Bravo AF: 0.237

Asia WGS AF: 0.136 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.40
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs2233204; hg19: chr3-39554786;