rs3212853

Variant names:

• chr19-50825538-C-G
• rs3212853
• ENST00000601680.1:n.1149G>C

Your query was ambiguous. Multiple possible variants found:

• chr19-50825538-C-G
• chr19-50825538-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000601680.1(KLK15):​n.1149G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000507 in 197,428 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000051 (0 hom.)
• Consequence: KLK15 ENST00000601680.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 0 publications found

Genes affected

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLK15	NM_017509.4	c.*258G>C		3_prime_UTR_variant	Exon 6 of 6	ENST00000598239.6	NP_059979.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLK15	ENST00000598239.6	c.*258G>C		3_prime_UTR_variant	Exon 6 of 6	1	NM_017509.4	ENSP00000469315.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000507 AC: 1 AN: 197428 Hom.: 0 Cov.: 2 AF XY: 0.00000989 AC XY: 1 AN XY: 101120

African (AFR) AF: 0.00 AC: 0 AN: 6436

American (AMR) AF: 0.00 AC: 0 AN: 7492

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6876

East Asian (EAS) AF: 0.00 AC: 0 AN: 14052

South Asian (SAS) AF: 0.00 AC: 0 AN: 13522

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12804

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 984

European-Non Finnish (NFE) AF: 0.00000814 AC: 1 AN: 122908

Other (OTH) AF: 0.00 AC: 0 AN: 12354

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs3212853; hg19: chr19-51328794;