rs12113878

Positions:

• chr7-139458699-C-G
• chr7-139458699-C-T

Variant summary

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

The NM_198508.4(KLRG2):​c.1006-4485G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,150 control chromosomes in the GnomAD database, including 4,385 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 0.23 (4385 hom., cov: 32)
• Consequence: KLRG2 NM_198508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

Genes affected

KLRG2 (HGNC:24778): (killer cell lectin like receptor G2) Predicted to enable carbohydrate binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KLRG2	NM_198508.4	c.1006-4485G>C		intron_variant		ENST00000340940.5	NP_940910.1
KLRG2	XM_005250311.4	c.1006-4992G>C		intron_variant			XP_005250368.1
KLRG2	XM_011516141.3	c.1005+20928G>C		intron_variant			XP_011514443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLRG2	ENST00000340940.5	c.1006-4485G>C		intron_variant		1	NM_198508.4	ENSP00000339356	P1
KLRG2	ENST00000393039.2	c.758-4992G>C		intron_variant		5		ENSP00000376759

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35692 AN: 152032 Hom.: 4377 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.235 AC: 35739 AN: 152150 Hom.: 4385 Cov.: 32 AF XY: 0.232 AC XY: 17284 AN XY: 74388

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.256

Alfa AF: 0.223 Hom.: 490

Bravo AF: 0.240

Asia WGS AF: 0.319 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.42

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: rs12113878; hg19: chr7-139143445;