rs2659108

Variant names:

• chr19-50896358-G-A
• rs2659108
• ENST00000597246.1:n.41C>T

Variant summary

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

The ENST00000597246.1(KLKP1):​n.41C>T 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 0.21 in 151,842 control chromosomes in the GnomAD database, including 5,706 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 0.21 (5704 hom., cov: 31)
  • Exomes 𝑓: 0.090 (2 hom.)
• Consequence: KLKP1 ENST00000597246.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

Genes affected

KLKP1 (HGNC:):

KLKP1 (HGNC:21260): (kallikrein pseudogene 1) Predicted to be located in cytoplasm and nucleus. [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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLKP1	NR_002948.1	n.41C>T		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLKP1	ENST00000597246.1	n.41C>T		non_coding_transcript_exon_variant	Exon 1 of 5	1

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31714 AN: 151352 Hom.: 5685 Cov.: 31

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0706

Gnomad EAS AF: 0.0255

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0478

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.169

GnomAD4 exome AF: 0.0897 AC: 33 AN: 368 Hom.: 2 Cov.: 0 AF XY: 0.0846 AC XY: 23 AN XY: 272

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.167 AC: 1 AN: 6

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 20

South Asian (SAS) AF: 0.00 AC: 0 AN: 14

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12

Middle Eastern (MID) AF: 0.250 AC: 1 AN: 4

European-Non Finnish (NFE) AF: 0.100 AC: 29 AN: 290

Other (OTH) AF: 0.100 AC: 2 AN: 20

GnomAD4 genome AF: 0.210 AC: 31785 AN: 151474 Hom.: 5704 Cov.: 31 AF XY: 0.203 AC XY: 15029 AN XY: 74004

African (AFR) AF: 0.493 AC: 20295 AN: 41194

American (AMR) AF: 0.133 AC: 2025 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0706 AC: 244 AN: 3454

East Asian (EAS) AF: 0.0254 AC: 130 AN: 5124

South Asian (SAS) AF: 0.165 AC: 788 AN: 4778

European-Finnish (FIN) AF: 0.0478 AC: 503 AN: 10518

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7286 AN: 67864

Other (OTH) AF: 0.173 AC: 363 AN: 2104

Alfa AF: 0.176 Hom.: 550

Bravo AF: 0.226

Asia WGS AF: 0.139 AC: 485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.28
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2659108; hg19: chr19-51399614;