rs16919034

chr9-97031301-A-Gchr9-97031301-A-T

Variant summary

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

The NM_001333.4(CTSV):c.*1648T>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 0.275 in 152,058 control chromosomes in the GnomAD database, including 8,056 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 0.27 (8055 hom., cov: 32)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: CTSV NM_001333.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

Genes affected

CTSV (HGNC:2538): (cathepsin V) The protein encoded by this gene, a member of the peptidase C1 family, is a lysosomal cysteine proteinase that may play an important role in corneal physiology. This gene is expressed in colorectal and breast carcinomas but not in normal colon, mammary gland, or peritumoral tissues, suggesting a possible role for this gene in tumor processes. Alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CTSV	NM_001333.4	c.*1648T>C		3_prime_UTR_variant	8/8	ENST00000259470.6
CTSV	NM_001201575.2	c.*1648T>C		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTSV	ENST00000259470.6	c.*1648T>C		3_prime_UTR_variant	8/8	1	NM_001333.4	P4

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41726 AN: 151936 Hom.: 8029 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.543

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.222

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 EAS exome AF: 1.00

GnomAD4 genome AF: 0.275 AC: 41797 AN: 152056 Hom.: 8055 Cov.: 32 AF XY: 0.281 AC XY: 20865 AN XY: 74332

Gnomad4 AFR AF: 0.515

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.144

Gnomad4 OTH AF: 0.223

Alfa AF: 0.169 Hom.: 2759

Bravo AF: 0.282

Asia WGS AF: 0.396 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.51
Dann	Benign	0.38

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: rs16919034; hg19: chr9-99793583;