rs4361859

chr9-97062415-G-Achr9-97062415-G-T

Variant summary

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

The ENST00000679551.1(CTSV):n.164-2444C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.766 in 152,156 control chromosomes in the GnomAD database, including 45,838 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 0.77 (45838 hom., cov: 33)
• Consequence: CTSV ENST00000679551.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CTSV	ENST00000679551.1	n.164-2444C>T		intron_variant, non_coding_transcript_variant
CTSV	ENST00000681517.1	n.315-2444C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.766 AC: 116484 AN: 152038 Hom.: 45788 Cov.: 33

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.756

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.766 AC: 116593 AN: 152156 Hom.: 45838 Cov.: 33 AF XY: 0.771 AC XY: 57352 AN XY: 74354

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.665

Gnomad4 OTH AF: 0.756

Alfa AF: 0.682 Hom.: 46921

Bravo AF: 0.778

Asia WGS AF: 0.867 AC: 3014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
Cadd	Benign	6.9
Dann	Benign	0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4361859; hg19: chr9-99824697;