rs470895

Positions:

• chr18-77003565-A-G

Variant summary

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

The NM_001025101.2(MBP):​c.576+13267T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,188 control chromosomes in the GnomAD database, including 2,324 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 0.16 (2324 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: MBP NM_001025101.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590

Genes affected

MBP (HGNC:6925): (myelin basic protein) The protein encoded by the classic MBP gene is a major constituent of the myelin sheath of oligodendrocytes and Schwann cells in the nervous system. However, MBP-related transcripts are also present in the bone marrow and the immune system. These mRNAs arise from the long MBP gene (otherwise called "Golli-MBP") that contains 3 additional exons located upstream of the classic MBP exons. Alternative splicing from the Golli and the MBP transcription start sites gives rise to 2 sets of MBP-related transcripts and gene products. The Golli mRNAs contain 3 exons unique to Golli-MBP, spliced in-frame to 1 or more MBP exons. They encode hybrid proteins that have N-terminal Golli aa sequence linked to MBP aa sequence. The second family of transcripts contain only MBP exons and produce the well characterized myelin basic proteins. This complex gene structure is conserved among species suggesting that the MBP transcription unit is an integral part of the Golli transcription unit and that this arrangement is important for the function and/or regulation of these genes. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MBP	NM_001025101.2	c.576+13267T>C		intron_variant		ENST00000355994.7	NP_001020272.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MBP	ENST00000355994.7	c.576+13267T>C		intron_variant		5	NM_001025101.2	ENSP00000348273	P1
	ENST00000624814.1	n.3282T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25021 AN: 152070 Hom.: 2315 Cov.: 33

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.0959

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0775

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.164

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.165 AC: 25065 AN: 152188 Hom.: 2324 Cov.: 33 AF XY: 0.164 AC XY: 12217 AN XY: 74394

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.0958

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0771

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.167

Alfa AF: 0.138 Hom.: 1476

Bravo AF: 0.164

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.55

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: rs470895; hg19: chr18-74715521;