rs2900420

chr12-10369195-G-Achr12-10369195-G-T

Variant summary

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

The NR_120430.1(KLRK1-AS1):n.266-4840G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,064 control chromosomes in the GnomAD database, including 2,312 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 0.17 (2312 hom., cov: 32)
• Consequence: KLRK1-AS1 NR_120430.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228

Genes affected

KLRK1-AS1 (HGNC:54868): (KLRK1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLRK1-AS1	NR_120430.1	n.266-4840G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLRK1-AS1	ENST00000500682.1	n.266-4840G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.171 AC: 26029 AN: 151946 Hom.: 2314 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.0660

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.171 AC: 26040 AN: 152064 Hom.: 2312 Cov.: 32 AF XY: 0.168 AC XY: 12463 AN XY: 74354

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.0662

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.187

Gnomad4 OTH AF: 0.162

Alfa AF: 0.177 Hom.: 939

Bravo AF: 0.168

Asia WGS AF: 0.117 AC: 402 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	5.7
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2900420; hg19: chr12-10521794;