Variant rs1805723 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_005810.4(KLRG1):c.66T>C(p.Tyr22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 1,599,442 control chromosomes in the GnomAD database, including 155,614 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 0.36 ( 10908 hom., cov: 33)

Exomes 𝑓: 0.44 ( 144706 hom. )

Consequence

KLRG1
NM_005810.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.457

Variant links:

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]

KLRG1 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BP7

Synonymous conserved (PhyloP=-0.457 with no splicing effect.

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/exons	MANE	Protein	UniProt
KLRG1	NM_005810.4 linkuse as main transcript	c.66T>C	p.Tyr22=	synonymous_variant	1/5	ENST00000356986.8	NP_005801.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLRG1	ENST00000356986.8 linkuse as main transcript	c.66T>C	p.Tyr22=	synonymous_variant	1/5	1	NM_005810.4	ENSP00000349477	P1	Q96E93-2
	ENST00000545706.1 linkuse as main transcript	n.71-1271A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.359

AC:

54634

AN:

152000

Hom.:

10899

Cov.:

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.373

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.398

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.471

Gnomad MID

AF:

0.415

Gnomad NFE

AF:

0.437

Gnomad OTH

AF:

0.374

GnomAD3 exomes

AF:

0.425

AC:

105128

AN:

247492

Hom.:

23151

AF XY:

0.429

AC XY:

57410

AN XY:

133948

show subpopulations

Gnomad AFR exome

AF:

0.167

Gnomad AMR exome

AF:

0.452

Gnomad ASJ exome

AF:

0.475

Gnomad EAS exome

AF:

0.383

Gnomad SAS exome

AF:

0.429

Gnomad FIN exome

AF:

0.473

Gnomad NFE exome

AF:

0.445

Gnomad OTH exome

AF:

0.453

GnomAD4 exome

AF:

0.443

AC:

641219

AN:

1447324

Hom.:

144706

Cov.:

AF XY:

0.443

AC XY:

318972

AN XY:

720774

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.447

Gnomad4 ASJ exome

AF:

0.477

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.431

Gnomad4 FIN exome

AF:

0.469

Gnomad4 NFE exome

AF:

0.451

Gnomad4 OTH exome

AF:

0.434

GnomAD4 genome

AF:

0.359

AC:

54674

AN:

152118

Hom.:

10908

Cov.:

AF XY:

0.361

AC XY:

26869

AN XY:

74336

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.373

Gnomad4 ASJ

AF:

0.472

Gnomad4 EAS

AF:

0.399

Gnomad4 SAS

AF:

0.439

Gnomad4 FIN

AF:

0.471

Gnomad4 NFE

AF:

0.437

Gnomad4 OTH

AF:

0.378

Alfa

AF:

0.422

Hom.:

14024

Bravo

AF:

0.346

Asia WGS

AF:

0.414

AC:

1443

AN:

3478

EpiCase

AF:

0.433

EpiControl

AF:

0.439

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.2

DANN

Benign

0.62

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over