rs13045348

Positions:

• chr20-4694943-T-C

Variant summary

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

The NM_000311.5(PRNP):​c.-10-4268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,002 control chromosomes in the GnomAD database, including 2,389 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 (2389 hom., cov: 31)
• Consequence: PRNP NM_000311.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.959

Genes affected

PRNP (HGNC:9449): (prion protein (Kanno blood group)) The protein encoded by this gene is a membrane glycosylphosphatidylinositol-anchored glycoprotein that tends to aggregate into rod-like structures. The encoded protein contains a highly unstable region of five tandem octapeptide repeats. This gene is found on chromosome 20, approximately 20 kbp upstream of a gene which encodes a biochemically and structurally similar protein to the one encoded by this gene. Mutations in the repeat region as well as elsewhere in this gene have been associated with Creutzfeldt-Jakob disease, fatal familial insomnia, Gerstmann-Straussler disease, Huntington disease-like 1, and kuru. An overlapping open reading frame has been found for this gene that encodes a smaller, structurally unrelated protein, AltPrp. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRNP	NM_000311.5	c.-10-4268T>C		intron_variant		ENST00000379440.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRNP	ENST00000379440.9	c.-10-4268T>C		intron_variant		1	NM_000311.5	P1
PRNP	ENST00000424424.2	c.-5-4273T>C		intron_variant		1		P1
PRNP	ENST00000430350.2	c.-10-4268T>C		intron_variant		1		P1
PRNP	ENST00000457586.2	c.-10-4268T>C		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24059 AN: 151884 Hom.: 2383 Cov.: 31

Gnomad AFR AF: 0.0440

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0198

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.158 AC: 24071 AN: 152002 Hom.: 2389 Cov.: 31 AF XY: 0.156 AC XY: 11583 AN XY: 74292

Gnomad4 AFR AF: 0.0439

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0199

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.179

Alfa AF: 0.207 Hom.: 2447

Bravo AF: 0.160

Asia WGS AF: 0.112 AC: 389 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.72
DANN	Benign	0.81

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: rs13045348; hg19: chr20-4675589;