rs3811942

Positions:

• chr5-96392736-A-G
• chr5-96392736-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_000439.5(PCSK1):​c.*265T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 505,378 control chromosomes in the GnomAD database, including 14,749 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.20 (3868 hom., cov: 32)
  • Exomes 𝑓: 0.24 (10881 hom.)
• Consequence: PCSK1 NM_000439.5 3_prime_UTR
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -0.343

Genes affected

PCSK1 (HGNC:8743): (proprotein convertase subtilisin/kexin type 1) 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 initial autocatalytic processing event in the ER to generate a heterodimer which exits the ER and sorts to subcellular compartments where a second autocatalytic even takes place and the catalytic activity is acquired. The protease is packaged into and activated in dense core secretory granules and expressed in the neuroendocrine system and brain. This gene encodes one of the seven basic amino acid-specific members which cleave their substrates at single or paired basic residues. It functions in the proteolytic activation of polypeptide hormones and neuropeptides precursors. Mutations in this gene have been associated with susceptibility to obesity and proprotein convertase 1/3 deficiency. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene [provided by RefSeq, Jan 2014]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 5-96392736-A-G is Benign according to our data. Variant chr5-96392736-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 354634.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PCSK1	NM_000439.5	c.*265T>C		3_prime_UTR_variant	14/14	ENST00000311106.8	NP_000430.3
LOC101929710	NR_130776.1	n.354+13084A>G		intron_variant, non_coding_transcript_variant
PCSK1	NM_001177875.2	c.*265T>C		3_prime_UTR_variant	14/14		NP_001171346.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PCSK1	ENST00000311106.8	c.*265T>C		3_prime_UTR_variant	14/14	1	NM_000439.5	ENSP00000308024	P1
	ENST00000502645.2	n.354+13084A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30792 AN: 152114 Hom.: 3867 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.206

GnomAD4 exome AF: 0.239 AC: 84369 AN: 353146 Hom.: 10881 Cov.: 2 AF XY: 0.237 AC XY: 44266 AN XY: 187016

Gnomad4 AFR exome AF: 0.0611

Gnomad4 AMR exome AF: 0.160

Gnomad4 ASJ exome AF: 0.184

Gnomad4 EAS exome AF: 0.180

Gnomad4 SAS exome AF: 0.187

Gnomad4 FIN exome AF: 0.364

Gnomad4 NFE exome AF: 0.261

Gnomad4 OTH exome AF: 0.231

GnomAD4 genome AF: 0.202 AC: 30795 AN: 152232 Hom.: 3868 Cov.: 32 AF XY: 0.206 AC XY: 15349 AN XY: 74406

Gnomad4 AFR AF: 0.0621

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.205

Alfa AF: 0.221 Hom.: 1868

Bravo AF: 0.180

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Obesity due to prohormone convertase I deficiency Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Monogenic Non-Syndromic Obesity Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.65

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: rs3811942; hg19: chr5-95728440; COSMIC: COSV60734403; COSMIC: COSV60734403;