rs7972757

Variant names:

• chr12-10393541-A-G
• rs7972757
• ENST00000539300.5:n.*75+269T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-10393541-A-G
• chr12-10393541-A-T

Variant summary

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

The ENST00000539300.5(KLRC4-KLRK1):​n.*75+269T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,178 control chromosomes in the GnomAD database, including 1,860 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 0.15 (1860 hom., cov: 32)
• Consequence: KLRC4-KLRK1 ENST00000539300.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 12 publications found

Genes affected

KLRC4-KLRK1 (HGNC:48357): (KLRC4-KLRK1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring KLRC4 (killer cell lectin-like receptor subfamily C, member 4) and KLRK1 (killer cell lectin-like receptor subfamily K, member 1) genes on chromosome 12. The read-through transcript includes an alternate 5' exon and lacks a significant portion of the KLRC4 coding sequence, including the start codon, and it thus encodes the KLRK1 protein. [provided by RefSeq, Dec 2010]

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539300.5. 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
	KLRC4-KLRK1	NM_001199805.1		c.-123+269T>C		intron	N/A	NP_001186734.1
	KLRK1-AS1	NR_120430.1		n.503-2638A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRC4-KLRK1	ENST00000539300.5	TSL:2	n.*75+269T>C		intron	N/A	ENSP00000455951.1
	KLRK1-AS1	ENST00000500682.1	TSL:2	n.503-2638A>G		intron	N/A
	KLRC4-KLRK1	ENST00000539370.5	TSL:2	n.469-4666T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22324 AN: 152060 Hom.: 1857 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.147 AC: 22347 AN: 152178 Hom.: 1860 Cov.: 32 AF XY: 0.151 AC XY: 11273 AN XY: 74414

African (AFR) AF: 0.181 AC: 7524 AN: 41510

American (AMR) AF: 0.164 AC: 2504 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 685 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1084 AN: 5178

South Asian (SAS) AF: 0.329 AC: 1586 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1419 AN: 10598

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7083 AN: 67984

Other (OTH) AF: 0.147 AC: 312 AN: 2116

Alfa AF: 0.127 Hom.: 823

Bravo AF: 0.149

Asia WGS AF: 0.256 AC: 887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		-0.11

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

Other links and lift over

dbSNP: rs7972757; hg19: chr12-10546140;