Variant rs8065610 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000674868.1(PMP22):c.-592G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 152,110 control chromosomes in the GnomAD database, including 8,372 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 0.32 ( 8372 hom., cov: 32)

Exomes 𝑓: 0.33 ( 0 hom. )

Consequence

PMP22
ENST00000674868.1 5_prime_UTR_premature_start_codon_gain

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.142

Variant links:

Genes affected

PMP22 (HGNC:9118): (peripheral myelin protein 22) This gene encodes an integral membrane protein that is a major component of myelin in the peripheral nervous system. Studies suggest two alternately used promoters drive tissue-specific expression. Various mutations of this gene are causes of Charcot-Marie-Tooth disease Type IA, Dejerine-Sottas syndrome, and hereditary neuropathy with liability to pressure palsies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

PMP22 links:

PMP22 (HGNC:):

PMP22 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
	use as main transcript	n.15272253C>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
PMP22	ENST00000674868.1 linkuse as main transcript	c.-592G>T	5_prime_UTR_premature_start_codon_gain_variant	1/5		ENSP00000502835.1	Q01453
PMP22	ENST00000674868.1 linkuse as main transcript	c.-592G>T	5_prime_UTR_variant	1/5		ENSP00000502835.1	Q01453
PMP22	ENST00000431343.1 linkuse as main transcript	n.38G>T	non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

49013

AN:

151980

Hom.:

8366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.240

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.281

Gnomad ASJ

AF:

0.326

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.371

Gnomad FIN

AF:

0.385

Gnomad MID

AF:

0.310

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.322

GnomAD4 exome

AF:

0.333

AC:

AN:

Hom.:

Cov.:

AF XY:

0.333

AC XY:

AN XY:

show subpopulations

Gnomad4 NFE exome

AF:

0.300

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.322

AC:

49032

AN:

152098

Hom.:

8372

Cov.:

AF XY:

0.320

AC XY:

23791

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.239

Gnomad4 AMR

AF:

0.281

Gnomad4 ASJ

AF:

0.326

Gnomad4 EAS

AF:

0.115

Gnomad4 SAS

AF:

0.372

Gnomad4 FIN

AF:

0.385

Gnomad4 NFE

AF:

0.387

Gnomad4 OTH

AF:

0.323

Alfa

AF:

0.361

Hom.:

14557

Bravo

AF:

0.309

Asia WGS

AF:

0.211

AC:

737

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

DANN

Benign

0.56

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over