3-39494393-A-G

Position:

• chr3-39494393-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393704.1(MOBP):​c.-4-7673A>G 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 151,612 control chromosomes in the GnomAD database, including 13,265 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 (13265 hom., cov: 32)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOBP	NM_001393704.1	c.-4-7673A>G		intron_variant		ENST00000684792.1	NP_001380633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOBP	ENST00000684792.1	c.-4-7673A>G		intron_variant			NM_001393704.1	ENSP00000508923

Frequencies

GnomAD3 genomes AF: 0.356 AC: 53918 AN: 151500 Hom.: 13225 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.356 AC: 54010 AN: 151612 Hom.: 13265 Cov.: 32 AF XY: 0.350 AC XY: 25896 AN XY: 74092

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.174

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.329

Alfa AF: 0.238 Hom.: 9856

Bravo AF: 0.375

Asia WGS AF: 0.337 AC: 1171 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.1
DANN	Benign	0.77

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

Publications

LitVar

Other links and lift over

dbSNP: rs535878; hg19: chr3-39535884;