rs562545

Positions:

• chr3-39495033-A-G
• chr3-39495033-A-T

Variant summary

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

The NM_001393704.1(MOBP):​c.-4-7033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,994 control chromosomes in the GnomAD database, including 36,773 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 0.68 (36773 hom., cov: 30)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

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]

(HGNC:):

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 = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOBP	NM_001393704.1	c.-4-7033A>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.-4-7033A>G		intron_variant			NM_001393704.1	ENSP00000508923
	ENST00000648447.1	n.1083T>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102940 AN: 151876 Hom.: 36714 Cov.: 30

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.678 AC: 103053 AN: 151994 Hom.: 36773 Cov.: 30 AF XY: 0.673 AC XY: 50004 AN XY: 74278

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.592

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.645

Alfa AF: 0.617 Hom.: 35123

Bravo AF: 0.683

Asia WGS AF: 0.516 AC: 1795 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	0.84
DANN	Benign	0.74

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: rs562545; hg19: chr3-39536524;