1-55058666-CGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT-CGTGTGTGTGTGTGTGTGTGTGTGTGTGT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2

The NM_174936.4(PCSK9):​c.1503+64_1503+71delGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00106 in 1,534,792 control chromosomes in the GnomAD database, including 10 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0037 ( 5 hom., cov: 0)
Exomes 𝑓: 0.00079 ( 5 hom. )

Consequence

PCSK9
NM_174936.4 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.564
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6
Variant 1-55058666-CGTGTGTGT-C is Benign according to our data. Variant chr1-55058666-CGTGTGTGT-C is described in ClinVar as [Likely_benign]. Clinvar id is 1568200.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr1-55058666-CGTGTGTGT-C is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00367 (523/142506) while in subpopulation AFR AF= 0.0126 (478/37860). AF 95% confidence interval is 0.0117. There are 5 homozygotes in gnomad4. There are 238 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 523 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PCSK9NM_174936.4 linkc.1503+64_1503+71delGTGTGTGT intron_variant ENST00000302118.5 NP_777596.2 Q8NBP7-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PCSK9ENST00000302118.5 linkc.1503+20_1503+27delGTGTGTGT intron_variant 1 NM_174936.4 ENSP00000303208.5 Q8NBP7-1

Frequencies

GnomAD3 genomes
AF:
0.00365
AC:
520
AN:
142426
Hom.:
5
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0126
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000617
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000219
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000505
Gnomad OTH
AF:
0.000514
GnomAD4 exome
AF:
0.000792
AC:
1102
AN:
1392286
Hom.:
5
AF XY:
0.000701
AC XY:
484
AN XY:
690340
show subpopulations
Gnomad4 AFR exome
AF:
0.0104
Gnomad4 AMR exome
AF:
0.000860
Gnomad4 ASJ exome
AF:
0.000684
Gnomad4 EAS exome
AF:
0.000270
Gnomad4 SAS exome
AF:
0.000160
Gnomad4 FIN exome
AF:
0.000479
Gnomad4 NFE exome
AF:
0.000566
Gnomad4 OTH exome
AF:
0.00116
GnomAD4 genome
AF:
0.00367
AC:
523
AN:
142506
Hom.:
5
Cov.:
0
AF XY:
0.00345
AC XY:
238
AN XY:
69042
show subpopulations
Gnomad4 AFR
AF:
0.0126
Gnomad4 AMR
AF:
0.000616
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000219
Gnomad4 NFE
AF:
0.000505
Gnomad4 OTH
AF:
0.000511

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Hypercholesterolemia, autosomal dominant, 3 Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 30, 2024- -

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.

Other links and lift over

dbSNP: rs35115360; hg19: chr1-55524339; API