chr12-10402080-T-C

Position:

• chr12-10402080-T-C

Variant summary

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

The NM_001199805.1(KLRC4-KLRK1):​c.-181+5556A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,942 control chromosomes in the GnomAD database, including 2,937 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 0.18 (2937 hom., cov: 32)
• Consequence: KLRC4-KLRK1 NM_001199805.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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]

KLRC4-KLRK1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLRC4-KLRK1	NM_001199805.1	c.-181+5556A>G		intron_variant			NP_001186734.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLRC4-KLRK1	ENST00000539300.5	n.*17+5556A>G		intron_variant		2		ENSP00000455951.1

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27905 AN: 151824 Hom.: 2933 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.184 AC: 27932 AN: 151942 Hom.: 2937 Cov.: 32 AF XY: 0.188 AC XY: 13946 AN XY: 74282

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.176

Alfa AF: 0.163 Hom.: 271

Bravo AF: 0.187

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.38

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: rs12821887; hg19: chr12-10554679;