4-155943599-C-A

Variant names:

• chr4-155943599-C-A
• rs11722604
• NM_001334.3:c.136-335G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001334.3(CTSO):​c.136-335G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,008 control chromosomes in the GnomAD database, including 2,525 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 0.16 (2525 hom., cov: 32)
• Consequence: CTSO NM_001334.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 2 publications found

Genes affected

CTSO (HGNC:2542): (cathepsin O) The protein encoded by the gene is a cysteine proteinase and a member of the papain superfamily. This proteolytic enzyme is involved in cellular protein degradation and turnover. The recombinant form of this enzyme was shown to degrade synthetic peptides typically used as substrates for cysteine proteinases and its proteolytic activity was abolished by an inhibitor of cyteine proteinase. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTSO	NM_001334.3	c.136-335G>T		intron_variant	Intron 1 of 7	ENST00000433477.4	NP_001325.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTSO	ENST00000433477.4	c.136-335G>T		intron_variant	Intron 1 of 7	1	NM_001334.3	ENSP00000414904.3

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24260 AN: 151890 Hom.: 2526 Cov.: 32

Gnomad AFR AF: 0.0435

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0922

Gnomad SAS AF: 0.0876

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.160 AC: 24254 AN: 152008 Hom.: 2525 Cov.: 32 AF XY: 0.154 AC XY: 11442 AN XY: 74284

African (AFR) AF: 0.0434 AC: 1802 AN: 41504

American (AMR) AF: 0.144 AC: 2194 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3472

East Asian (EAS) AF: 0.0913 AC: 472 AN: 5170

South Asian (SAS) AF: 0.0879 AC: 424 AN: 4824

European-Finnish (FIN) AF: 0.177 AC: 1868 AN: 10530

Middle Eastern (MID) AF: 0.0685 AC: 20 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16392 AN: 67926

Other (OTH) AF: 0.143 AC: 301 AN: 2106

Alfa AF: 0.121 Hom.: 262

Bravo AF: 0.154

Asia WGS AF: 0.0920 AC: 322 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		0.012
Mutation Taster		=100/0	polymorphism (auto)

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: rs11722604; hg19: chr4-156864751;