ENST00000326856.8:c.-32+2178A>G

Variant names:

• chr19-50834937-T-C
• rs190552
• ENST00000326856.8:c.-32+2178A>G

Variant summary

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

The ENST00000326856.8(KLK15):​c.-32+2178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,094 control chromosomes in the GnomAD database, including 4,815 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 0.24 (4815 hom., cov: 31)
• Consequence: KLK15 ENST00000326856.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660
• Publications: 7 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]

ENSG00000267968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.213+3644T>C		intron_variant	Intron 2 of 2
LOC105372441	NR_131205.1	n.230+3644T>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLK15	ENST00000326856.8	c.-32+2178A>G		intron_variant	Intron 1 of 5	5		ENSP00000314783.4
ENSG00000267968	ENST00000598079.1	n.213+3644T>C		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37200 AN: 151976 Hom.: 4814 Cov.: 31

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.245 AC: 37216 AN: 152094 Hom.: 4815 Cov.: 31 AF XY: 0.245 AC XY: 18183 AN XY: 74354

African (AFR) AF: 0.308 AC: 12764 AN: 41478

American (AMR) AF: 0.213 AC: 3250 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3470

East Asian (EAS) AF: 0.113 AC: 584 AN: 5186

South Asian (SAS) AF: 0.174 AC: 837 AN: 4816

European-Finnish (FIN) AF: 0.230 AC: 2431 AN: 10584

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15334 AN: 67972

Other (OTH) AF: 0.273 AC: 576 AN: 2110

Alfa AF: 0.235 Hom.: 1467

Bravo AF: 0.250

Asia WGS AF: 0.143 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.0
DANN	Benign	0.69
PhyloP100		0.66
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs190552; hg19: chr19-51338193;