rs16919034

Variant names:

• chr9-97031301-A-G
• rs16919034
• NM_001333.4:c.*1648T>C

Your query was ambiguous. Multiple possible variants found:

• chr9-97031301-A-G
• chr9-97031301-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CTSV	NM_001333.4	c.*1648T>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000259470.6	NP_001324.2
CTSV	NM_001201575.2	c.*1648T>C		3_prime_UTR_variant	Exon 8 of 8		NP_001188504.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTSV	ENST00000259470.6	c.*1648T>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_001333.4	ENSP00000259470.5

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.515 AC: 21324 AN: 41442

American (AMR) AF: 0.181 AC: 2764 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3472

East Asian (EAS) AF: 0.543 AC: 2803 AN: 5166

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4818

European-Finnish (FIN) AF: 0.247 AC: 2612 AN: 10580

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9815 AN: 67978

Other (OTH) AF: 0.223 AC: 471 AN: 2116

Alfa AF: 0.182 Hom.: 4338

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
PhyloP100		-0.91

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

Other links and lift over

dbSNP: rs16919034; hg19: chr9-99793583;