rs1903860

chr10-87860453-T-C

Variant summary

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

The NM_001126049.2(KLLN):c.*1498A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,292 control chromosomes in the GnomAD database, including 1,551 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 0.13 (1551 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KLLN NM_001126049.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

KLLN (HGNC:37212): (killin, p53 regulated DNA replication inhibitor) The protein encoded by this intronless gene is found in the nucleus, where it can inhibit DNA synthesis and promote S phase arrest coupled to apoptosis. The expression of this DNA binding protein is upregulated by transcription factor p53. [provided by RefSeq, Dec 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLLN	NM_001126049.2	c.*1498A>G		3_prime_UTR_variant	1/1	ENST00000445946.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLLN	ENST00000445946.5	c.*1498A>G		3_prime_UTR_variant	1/1		NM_001126049.2	P1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19588 AN: 152174 Hom.: 1545 Cov.: 32

Gnomad AFR AF: 0.0700

Gnomad AMI AF: 0.0584

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.139

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 20 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 14

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.129 AC: 19614 AN: 152292 Hom.: 1551 Cov.: 32 AF XY: 0.129 AC XY: 9633 AN XY: 74468

Gnomad4 AFR AF: 0.0704

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.351

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.138

Alfa AF: 0.130 Hom.: 182

Bravo AF: 0.135

Asia WGS AF: 0.225 AC: 782 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.3
Dann	Benign	0.85

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1903860; hg19: chr10-89620210;