rs10512189

Positions:

• chr9-87775842-T-C

Variant summary

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

The NR_027917.1(CTSL3P):​n.425+2198T>C 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 0.0282 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 NR_027917.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.872

Genes affected

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
CTSL3P	NR_027917.1	n.425+2198T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTSL3P	ENST00000354530.2	n.425+2198T>C		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.0689

Gnomad4 ASJ AF: 0.000866

Gnomad4 EAS AF: 0.000773

Gnomad4 SAS AF: 0.0357

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.00276

Gnomad4 OTH AF: 0.0293

Alfa AF: 0.0199 Hom.: 16

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512189; hg19: chr9-90390757;