ENST00000500682.1:n.265+4757G>T

Variant names:

• chr12-10368790-G-T
• rs10743889
• ENST00000500682.1:n.265+4757G>T

Variant summary

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

The ENST00000500682.1(KLRK1-AS1):​n.265+4757G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.774 in 151,624 control chromosomes in the GnomAD database, including 45,628 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 0.77 (45628 hom., cov: 29)
• Consequence: KLRK1-AS1 ENST00000500682.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 8 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.8 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.265+4757G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRK1-AS1	ENST00000500682.1	TSL:2	n.265+4757G>T		intron	N/A
	KLRK1-AS1	ENST00000654540.2		n.224+261G>T		intron	N/A
	KLRK1-AS1	ENST00000663376.2		n.239+4757G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.774 AC: 117292 AN: 151506 Hom.: 45610 Cov.: 29

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.774 AC: 117355 AN: 151624 Hom.: 45628 Cov.: 29 AF XY: 0.769 AC XY: 56907 AN XY: 74032

African (AFR) AF: 0.770 AC: 31799 AN: 41282

American (AMR) AF: 0.708 AC: 10799 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.771 AC: 2674 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3666 AN: 5140

South Asian (SAS) AF: 0.642 AC: 3083 AN: 4802

European-Finnish (FIN) AF: 0.770 AC: 8021 AN: 10422

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54757 AN: 67938

Other (OTH) AF: 0.777 AC: 1642 AN: 2112

Alfa AF: 0.791 Hom.: 84657

Bravo AF: 0.769

Asia WGS AF: 0.686 AC: 2388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.39
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10743889; hg19: chr12-10521389;