rs2889717

Variant names:

• chr12-9134205-T-C
• rs2889717
• XM_017018684.2:c.*34-881T>C

Variant summary

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

The ENST00000839050.1(ENSG00000309149):​n.81-881T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 152,254 control chromosomes in the GnomAD database, including 160 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 0.022 (160 hom., cov: 32)
• Consequence: ENSG00000309149 ENST00000839050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• Publications: 4 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]

ENSG00000309149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839050.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309149	ENST00000839050.1		n.81-881T>C		intron	N/A
	ENSG00000309149	ENST00000839051.1		n.335+5570T>C		intron	N/A
	ENSG00000309236	ENST00000839766.1		n.*183A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0220 AC: 3348 AN: 152136 Hom.: 156 Cov.: 32

Gnomad AFR AF: 0.00524

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.0817

Gnomad ASJ AF: 0.0147

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.0844

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00700

Gnomad OTH AF: 0.0320

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

GnomAD4 genome AF: 0.0221 AC: 3359 AN: 152254 Hom.: 160 Cov.: 32 AF XY: 0.0252 AC XY: 1874 AN XY: 74454

African (AFR) AF: 0.00522 AC: 217 AN: 41564

American (AMR) AF: 0.0826 AC: 1264 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0147 AC: 51 AN: 3472

East Asian (EAS) AF: 0.149 AC: 769 AN: 5176

South Asian (SAS) AF: 0.0841 AC: 405 AN: 4816

European-Finnish (FIN) AF: 0.00151 AC: 16 AN: 10612

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00699 AC: 475 AN: 68000

Other (OTH) AF: 0.0317 AC: 67 AN: 2116

Alfa AF: 0.0110 Hom.: 5

Bravo AF: 0.0290

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.45
PhyloP100		0.084

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2889717;

hg19: chr12-9286801;