rs2080117

Variant names:

• chr12-8985745-C-T
• rs2080117
• NM_001329101.2:c.-155-6461C>T

Variant summary

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

The NM_001329101.2(KLRG1):​c.-155-6461C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,020 control chromosomes in the GnomAD database, including 10,568 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 0.35 (10568 hom., cov: 31)
• Consequence: KLRG1 NM_001329101.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 2 publications found

Genes affected

KLRG1 (HGNC:6380): (killer cell lectin like receptor G1) Natural killer (NK) cells are lymphocytes that can mediate lysis of certain tumor cells and virus-infected cells without previous activation. They can also regulate specific humoral and cell-mediated immunity. The protein encoded by this gene belongs to the killer cell lectin-like receptor (KLR) family, which is a group of transmembrane proteins preferentially expressed in NK cells. Studies in mice suggested that the expression of this gene may be regulated by MHC class I molecules. [provided by RefSeq, Jun 2016]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLRG1	NM_001329101.2	c.-155-6461C>T		intron_variant	Intron 1 of 4		NP_001316030.1
KLRG1	NM_001329102.2	c.-289-4467C>T		intron_variant	Intron 1 of 5		NP_001316031.1
KLRG1	NM_001329103.2	c.-155-6461C>T		intron_variant	Intron 1 of 4		NP_001316032.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLRG1	ENST00000539240.5	c.-155-6461C>T		intron_variant	Intron 1 of 4	3		ENSP00000445627.1
KLRG1	ENST00000538029.1	n.113-23230C>T		intron_variant	Intron 1 of 2	2
KLRG1	ENST00000541957.1	n.248-4467C>T		intron_variant	Intron 2 of 3	4
KLRG1	ENST00000544226.5	n.131-6461C>T		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52714 AN: 151902 Hom.: 10564 Cov.: 31

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.361

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

GnomAD4 genome AF: 0.347 AC: 52723 AN: 152020 Hom.: 10568 Cov.: 31 AF XY: 0.350 AC XY: 25982 AN XY: 74298

African (AFR) AF: 0.133 AC: 5504 AN: 41504

American (AMR) AF: 0.368 AC: 5611 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2055 AN: 5166

South Asian (SAS) AF: 0.439 AC: 2117 AN: 4826

European-Finnish (FIN) AF: 0.472 AC: 4973 AN: 10536

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29677 AN: 67938

Other (OTH) AF: 0.365 AC: 769 AN: 2106

Alfa AF: 0.368 Hom.: 1484

Bravo AF: 0.331

Asia WGS AF: 0.405 AC: 1412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.29
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2080117; hg19: chr12-9138341;