ENST00000500682.1:n.266-4840G>A

Variant names:

• chr12-10369195-G-A
• rs2900420
• ENST00000500682.1:n.266-4840G>A

Variant summary

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

The ENST00000500682.1(KLRK1-AS1):​n.266-4840G>A variant causes a intron 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 ENST00000500682.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500682.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRK1-AS1	NR_120430.1		n.266-4840G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRK1-AS1	ENST00000500682.1	TSL:2	n.266-4840G>A		intron	N/A
	KLRK1-AS1	ENST00000654540.2		n.224+666G>A		intron	N/A
	KLRK1-AS1	ENST00000663376.2		n.240-4840G>A		intron	N/A

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

African (AFR) AF: 0.182 AC: 7553 AN: 41464

American (AMR) AF: 0.128 AC: 1960 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3470

East Asian (EAS) AF: 0.0662 AC: 343 AN: 5182

South Asian (SAS) AF: 0.125 AC: 602 AN: 4826

European-Finnish (FIN) AF: 0.142 AC: 1496 AN: 10558

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12732 AN: 67958

Other (OTH) AF: 0.162 AC: 343 AN: 2114

Alfa AF: 0.177 Hom.: 1912

Bravo AF: 0.168

Asia WGS AF: 0.117 AC: 402 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.18
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs2900420; hg19: chr12-10521794;