rs2889717

chr12-9134205-T-C

Variant summary

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

The XM_017018684.2(KLRG1):c.*34-881T>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: KLRG1 XM_017018684.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

Genes affected

KLRG1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLRG1	XM_017018684.2	c.*34-881T>C		intron_variant
KLRG1	XM_017018685.2	c.*33+76039T>C		intron_variant
KLRG1	XM_047428074.1	c.*34-59850T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.00522

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.0147

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.0841

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.00699

Gnomad4 OTH AF: 0.0317

Alfa AF: 0.0128 Hom.: 3

Bravo AF: 0.0290

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.1
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2889717; hg19: chr12-9286801;