Variant chrX-103783933-G-GTATATATACATATATTTA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BA1

The NM_000533.5(PLP1):c.5-1636_5-1619dup variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.12 ( 726 hom., 3087 hem., cov: 19)

Consequence

PLP1
NM_000533.5 intron

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.21

Variant links:

Genes affected

PLP1 (HGNC:9086): (proteolipid protein 1) This gene encodes a transmembrane proteolipid protein that is the predominant component of myelin. The encoded protein may play a role in the compaction, stabilization, and maintenance of myelin sheaths, as well as in oligodendrocyte development and axonal survival. Mutations in this gene cause Pelizaeus-Merzbacher disease and spastic paraplegia type 2. Alternatively splicing results in multiple transcript variants, including the DM20 splice variant. [provided by RefSeq, Feb 2015]

PLP1 links:

RAB9B (HGNC:):

RAB9B links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant X-103783933-G-GTATATATACATATATTTA is Benign according to our data. Variant chrX-103783933-G-GTATATATACATATATTTA is described in ClinVar as [Benign]. Clinvar id is 691855.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLP1	NM_000533.5 linkuse as main transcript	c.5-1636_5-1619dup		intron_variant		ENST00000621218.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLP1	ENST00000621218.5 linkuse as main transcript	c.5-1636_5-1619dup		intron_variant		1	NM_000533.5	P1	P60201-1

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

13236

AN:

110316

Hom.:

727

Cov.:

AF XY:

0.0940

AC XY:

3090

AN XY:

32888

show subpopulations

Gnomad AFR

AF:

0.146

Gnomad AMI

AF:

0.0990

Gnomad AMR

AF:

0.0812

Gnomad ASJ

AF:

0.142

Gnomad EAS

AF:

0.000555

Gnomad SAS

AF:

0.0197

Gnomad FIN

AF:

0.0763

Gnomad MID

AF:

0.284

Gnomad NFE

AF:

0.129

Gnomad OTH

AF:

0.124

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

GnomAD4 genome

AF:

0.120

AC:

13228

AN:

110353

Hom.:

726

Cov.:

AF XY:

0.0937

AC XY:

3087

AN XY:

32937

show subpopulations

Gnomad4 AFR

AF:

0.145

Gnomad4 AMR

AF:

0.0810

Gnomad4 ASJ

AF:

0.142

Gnomad4 EAS

AF:

0.000556

Gnomad4 SAS

AF:

0.0198

Gnomad4 FIN

AF:

0.0763

Gnomad4 NFE

AF:

0.129

Gnomad4 OTH

AF:

0.122

Alfa

AF:

0.130

Hom.:

631

Asia WGS

AF:

0.0320

AC:

AN:

2519

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, no assertion criteria provided

research

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

This variant was dentified in a patient with an Xq22del, and noted in the context of the Xq22del mechanism of formation, but not believed to be indepdently causative of the observed phenotype. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over