rs266854

chr19-50834562-A-Cchr19-50834562-A-T

Variant summary

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

The NR_131205.1(LOC105372441):n.230+3269A>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 0.709 in 151,980 control chromosomes in the GnomAD database, including 38,291 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 0.71 (38291 hom., cov: 31)
• Consequence: LOC105372441 NR_131205.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

Genes affected

(HGNC:):

KLK15 (HGNC:20453): (kallikrein related peptidase 15) Kallikreins are a subgroup of serine proteases having diverse physiological functions. Growing evidence suggests that many kallikreins are implicated in carcinogenesis and some have potential as novel cancer and other disease biomarkers. This gene is one of the fifteen kallikrein subfamily members located in a cluster on chromosome 19. In prostate cancer, this gene has increased expression, which indicates its possible use as a diagnostic or prognostic marker for prostate cancer. The gene contains multiple polyadenylation sites and alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372441	NR_131205.1	n.230+3269A>C		intron_variant, non_coding_transcript_variant
LOC105372441	NR_131203.1	n.213+3269A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000598079.1	n.213+3269A>C		intron_variant, non_coding_transcript_variant		3
KLK15	ENST00000326856.8	c.-32+2553T>G		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107721 AN: 151862 Hom.: 38254 Cov.: 31

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.709 AC: 107804 AN: 151980 Hom.: 38291 Cov.: 31 AF XY: 0.714 AC XY: 53025 AN XY: 74298

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.819

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.715

Gnomad4 OTH AF: 0.749

Alfa AF: 0.724 Hom.: 4971

Bravo AF: 0.701

Asia WGS AF: 0.667 AC: 2323 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	1.7
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs266854; hg19: chr19-51337818;