rs6809442

chr3-39517666-G-A

Variant summary

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

The ENST00000424090.5(MOBP):c.*258+4060G>A variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOBP	NR_003090.3	n.579+4060G>A		intron_variant, non_coding_transcript_variant
MOBP	NR_103504.2	n.921+4060G>A		intron_variant, non_coding_transcript_variant
MOBP	NR_103505.2	n.959+4060G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOBP	ENST00000424090.5	c.*258+4060G>A		intron_variant, NMD_transcript_variant		1
MOBP	ENST00000442631.5	c.*223+4060G>A		intron_variant, NMD_transcript_variant		1
MOBP	ENST00000452959.6	c.*184+4060G>A		intron_variant, NMD_transcript_variant		1
MOBP	ENST00000479860.1	n.286-57G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.667

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.771

Gnomad4 OTH AF: 0.631

Alfa AF: 0.708 Hom.: 16919

Bravo AF: 0.582

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	4.5
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6809442; hg19: chr3-39559157;