3-39512297-C-T

Variant names:

• chr3-39512297-C-T
• rs816488
• ENST00000383754.7:c.207-1086C>T

Variant summary

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

The NM_001278322.2(MOBP):​c.621-1086C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,230 control chromosomes in the GnomAD database, including 66,816 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 0.93 (66816 hom., cov: 31)
• Consequence: MOBP NM_001278322.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

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 (NFE) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOBP	NM_001278322.2	c.621-1086C>T		intron_variant	Intron 4 of 4		NP_001265251.1
MOBP	NM_182935.4	c.207-1086C>T		intron_variant	Intron 3 of 3		NP_891980.1
MOBP	NR_003090.3	n.356-1086C>T		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOBP	ENST00000383754.7	c.207-1086C>T		intron_variant	Intron 3 of 3	1		ENSP00000373261.3
MOBP	ENST00000424090.5	n.*35-1086C>T		intron_variant	Intron 2 of 4	1		ENSP00000389055.1
MOBP	ENST00000442631.5	n.549-1086C>T		intron_variant	Intron 2 of 4	1		ENSP00000413771.1

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142222 AN: 152112 Hom.: 66780 Cov.: 31

Gnomad AFR AF: 0.850

Gnomad AMI AF: 0.993

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.978

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.935 AC: 142312 AN: 152230 Hom.: 66816 Cov.: 31 AF XY: 0.935 AC XY: 69617 AN XY: 74460

Gnomad4 AFR AF: 0.849

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.920

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.994

Gnomad4 NFE AF: 0.978

Gnomad4 OTH AF: 0.936

Alfa AF: 0.963 Hom.: 71452

Bravo AF: 0.928

Asia WGS AF: 0.871 AC: 3032 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
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: rs816488; hg19: chr3-39553788;