rs2659108

chr19-50896358-G-A

Variant summary

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

The NR_002948.1(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 NR_002948.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

KLKP1 (HGNC:21260): (kallikrein pseudogene 1) Predicted to be located in cytoplasm and nucleus. [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=-0.96).
• 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/exons	MANE	UniProt
KLKP1	NR_002948.1	n.41C>T		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLKP1	ENST00000597246.1	n.41C>T		non_coding_transcript_exon_variant	1/5	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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.167

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.100

Gnomad4 OTH exome AF: 0.100

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

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0706

Gnomad4 EAS AF: 0.0254

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.0478

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.173

Alfa AF: 0.165 Hom.: 468

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2659108; hg19: chr19-51399614;