rs6809442

Variant names:

• chr3-39517666-G-A
• rs6809442
• ENST00000424090.5:n.*258+4060G>A

Variant summary

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

The ENST00000424090.5(MOBP):​n.*258+4060G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.607 in 152,004 control chromosomes in the GnomAD database, including 32,383 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 0.61 (32383 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: MOBP ENST00000424090.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214
• 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424090.5. 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	NR_003090.3		n.579+4060G>A		intron	N/A
	MOBP	NR_103504.2		n.921+4060G>A		intron	N/A
	MOBP	NR_103505.2		n.959+4060G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOBP	ENST00000424090.5	TSL:1	n.*258+4060G>A		intron	N/A	ENSP00000389055.1
	MOBP	ENST00000442631.5	TSL:1	n.*223+4060G>A		intron	N/A	ENSP00000413771.1
	MOBP	ENST00000452959.6	TSL:1	n.*184+4060G>A		intron	N/A	ENSP00000405549.1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92311 AN: 151886 Hom.: 32389 Cov.: 31

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.771

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.607 AC: 92309 AN: 152004 Hom.: 32383 Cov.: 31 AF XY: 0.612 AC XY: 45454 AN XY: 74300

African (AFR) AF: 0.229 AC: 9467 AN: 41412

American (AMR) AF: 0.683 AC: 10429 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2505 AN: 3468

East Asian (EAS) AF: 0.667 AC: 3447 AN: 5168

South Asian (SAS) AF: 0.675 AC: 3249 AN: 4812

European-Finnish (FIN) AF: 0.797 AC: 8424 AN: 10574

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.771 AC: 52436 AN: 67974

Other (OTH) AF: 0.631 AC: 1332 AN: 2112

Alfa AF: 0.698 Hom.: 19702

Bravo AF: 0.582

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.5
DANN	Benign	0.34
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6809442; hg19: chr3-39559157;