chr3-39500688-C-A

Variant names:

• chr3-39500688-C-A
• rs1768244
• NM_001393704.1:c.-4-1378C>A

Variant summary

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

The NM_001393704.1(MOBP):​c.-4-1378C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,824 control chromosomes in the GnomAD database, including 12,761 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 0.35 (12761 hom., cov: 31)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 3 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOBP	NM_001393704.1	c.-4-1378C>A		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.-4-1378C>A		intron_variant	Intron 2 of 3		NM_001393704.1	ENSP00000508923.1

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53590 AN: 151706 Hom.: 12711 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.0870

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.354 AC: 53706 AN: 151824 Hom.: 12761 Cov.: 31 AF XY: 0.350 AC XY: 26004 AN XY: 74218

African (AFR) AF: 0.681 AC: 28176 AN: 41378

American (AMR) AF: 0.287 AC: 4384 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1565 AN: 5158

South Asian (SAS) AF: 0.317 AC: 1522 AN: 4806

European-Finnish (FIN) AF: 0.198 AC: 2091 AN: 10548

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14142 AN: 67904

Other (OTH) AF: 0.339 AC: 714 AN: 2108

Alfa AF: 0.447 Hom.: 4454

Bravo AF: 0.374

Asia WGS AF: 0.353 AC: 1226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.32
PhyloP100		0.33
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: rs1768244; hg19: chr3-39542179;