chr9-87775842-T-C

Variant names:

• chr9-87775842-T-C
• rs10512189
• ENST00000354530.2:n.425+2198T>C

Variant summary

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

The ENST00000354530.2(CTSL3P):​n.425+2198T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0282 in 152,250 control chromosomes in the GnomAD database, including 155 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 0.028 (155 hom., cov: 32)
• Consequence: CTSL3P ENST00000354530.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872
• Publications: 1 publications found

Genes affected

CTSL3P (HGNC:):

CTSL3P (HGNC:33132): (cathepsin L family member 3, pseudogene) Predicted to enable cysteine-type endopeptidase activity. Predicted to be involved in proteolysis involved in cellular protein catabolic process. Predicted to be active in extracellular space and lysosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CTSL3P	NR_027917.1	n.425+2198T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CTSL3P	ENST00000354530.2	n.425+2198T>C		intron_variant	Intron 3 of 4	1

Frequencies

GnomAD3 genomes AF: 0.0281 AC: 4273 AN: 152132 Hom.: 152 Cov.: 32

Gnomad AFR AF: 0.0666

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0685

Gnomad ASJ AF: 0.000866

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00278

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0282 AC: 4287 AN: 152250 Hom.: 155 Cov.: 32 AF XY: 0.0292 AC XY: 2173 AN XY: 74442

African (AFR) AF: 0.0665 AC: 2763 AN: 41530

American (AMR) AF: 0.0689 AC: 1054 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.000866 AC: 3 AN: 3466

East Asian (EAS) AF: 0.000773 AC: 4 AN: 5176

South Asian (SAS) AF: 0.0357 AC: 172 AN: 4814

European-Finnish (FIN) AF: 0.00358 AC: 38 AN: 10620

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00276 AC: 188 AN: 68022

Other (OTH) AF: 0.0293 AC: 62 AN: 2114

Alfa AF: 0.0211 Hom.: 18

Bravo AF: 0.0342

Asia WGS AF: 0.0210 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.39
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs10512189; hg19: chr9-90390757;