rs562545

Variant names:

• chr3-39495033-A-G
• rs562545
• NM_001393704.1:c.-4-7033A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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]

ENSG00000285885 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MOBP	NM_001393704.1	c.-4-7033A>G		intron_variant	Intron 2 of 3	ENST00000684792.1	NP_001380633.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOBP	ENST00000684792.1	c.-4-7033A>G		intron_variant	Intron 2 of 3		NM_001393704.1	ENSP00000508923.1

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

African (AFR) AF: 0.915 AC: 37938 AN: 41466

American (AMR) AF: 0.549 AC: 8395 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2066 AN: 3468

East Asian (EAS) AF: 0.398 AC: 2053 AN: 5154

South Asian (SAS) AF: 0.603 AC: 2902 AN: 4814

European-Finnish (FIN) AF: 0.592 AC: 6246 AN: 10552

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41534 AN: 67952

Other (OTH) AF: 0.645 AC: 1353 AN: 2098

Alfa AF: 0.620 Hom.: 41030

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
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs562545; hg19: chr3-39536524;