rs12067569

chr1-55062956-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The NM_174936.4(PCSK9):c.1864-413G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0788 in 152,014 control chromosomes in the GnomAD database, including 827 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.079 (827 hom., cov: 32)
• Consequence: PCSK9 NM_174936.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660

Genes affected

PCSK9 (HGNC:20001): (proprotein convertase subtilisin/kexin type 9) This gene encodes a member of the subtilisin-like proprotein convertase family, which includes proteases that process protein and peptide precursors trafficking through regulated or constitutive branches of the secretory pathway. The encoded protein undergoes an autocatalytic processing event with its prosegment in the ER and is constitutively secreted as an inactive protease into the extracellular matrix and trans-Golgi network. It is expressed in liver, intestine and kidney tissues and escorts specific receptors for lysosomal degradation. It plays a role in cholesterol and fatty acid metabolism. Mutations in this gene have been associated with autosomal dominant familial hypercholesterolemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 1-55062956-G-A is Benign according to our data. Variant chr1-55062956-G-A is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PCSK9	NM_174936.4	c.1864-413G>A		intron_variant		ENST00000302118.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PCSK9	ENST00000302118.5	c.1864-413G>A		intron_variant		1	NM_174936.4	P2

Frequencies

GnomAD3 genomes AF: 0.0786 AC: 11944 AN: 151896 Hom.: 825 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0370

Gnomad ASJ AF: 0.0490

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0313

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0349

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0788 AC: 11986 AN: 152014 Hom.: 827 Cov.: 32 AF XY: 0.0764 AC XY: 5679 AN XY: 74336

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0369

Gnomad4 ASJ AF: 0.0490

Gnomad4 EAS AF: 0.0496

Gnomad4 SAS AF: 0.0221

Gnomad4 FIN AF: 0.0313

Gnomad4 NFE AF: 0.0350

Gnomad4 OTH AF: 0.0560

Alfa AF: 0.0702 Hom.: 115

Bravo AF: 0.0852

Asia WGS AF: 0.0450 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	14
Dann	Benign	0.84

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: rs12067569; hg19: chr1-55528629;