20-23628343-C-T

Position:

• chr20-23628343-C-T

Variant summary

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

The ENST00000398411.5(CST3):​c.*1125G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.487 in 152,144 control chromosomes in the GnomAD database, including 21,499 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 0.49 (21496 hom., cov: 33)
  • Exomes 𝑓: 0.57 (3 hom.)
• Consequence: CST3 ENST00000398411.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

Genes affected

CST3 (HGNC:2475): (cystatin C) The cystatin superfamily encompasses proteins that contain multiple cystatin-like sequences. Some of the members are active cysteine protease inhibitors, while others have lost or perhaps never acquired this inhibitory activity. There are three inhibitory families in the superfamily, including the type 1 cystatins (stefins), type 2 cystatins and the kininogens. The type 2 cystatin proteins are a class of cysteine proteinase inhibitors found in a variety of human fluids and secretions, where they appear to provide protective functions. The cystatin locus on chromosome 20 contains the majority of the type 2 cystatin genes and pseudogenes. This gene is located in the cystatin locus and encodes the most abundant extracellular inhibitor of cysteine proteases, which is found in high concentrations in biological fluids and is expressed in virtually all organs of the body. A mutation in this gene has been associated with amyloid angiopathy. Expression of this protein in vascular wall smooth muscle cells is severely reduced in both atherosclerotic and aneurysmal aortic lesions, establishing its role in vascular disease. In addition, this protein has been shown to have an antimicrobial function, inhibiting the replication of herpes simplex virus. Alternative splicing results in multiple transcript variants encoding a single protein. [provided by RefSeq, Nov 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CST3	NM_001288614.2	c.*1125G>A		3_prime_UTR_variant	4/4		NP_001275543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CST3	ENST00000398411.5	c.*1125G>A		3_prime_UTR_variant	4/4	1		ENSP00000381448	P1

Frequencies

GnomAD3 genomes AF: 0.487 AC: 74014 AN: 152012 Hom.: 21489 Cov.: 33

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.612

Gnomad OTH AF: 0.529

GnomAD4 exome AF: 0.571 AC: 8 AN: 14 Hom.: 3 Cov.: 0 AF XY: 0.667 AC XY: 8 AN XY: 12

Gnomad4 AFR exome AF: 0.00

Gnomad4 NFE exome AF: 0.667

GnomAD4 genome AF: 0.487 AC: 74025 AN: 152130 Hom.: 21496 Cov.: 33 AF XY: 0.493 AC XY: 36685 AN XY: 74396

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.612

Gnomad4 OTH AF: 0.526

Alfa AF: 0.514 Hom.: 4200

Bravo AF: 0.472

Asia WGS AF: 0.533 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.34

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: rs2424574; hg19: chr20-23608980;