Genetic Variant KLRG2:p.Arg202Gln (chr7-139483038-C-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_198508.4(KLRG2):c.605G>A(p.Arg202Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R202W) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

KLRG2
NM_198508.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0830

Publications

0 publications found

Variant links:

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]

KLRG2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.07399419).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLRG2	NM_198508.4 link	c.605G>A	p.Arg202Gln	missense_variant	Exon 1 of 5	ENST00000340940.5	NP_940910.1	A4D1S0-1
KLRG2	XM_011516140.3 link	c.605G>A	p.Arg202Gln	missense_variant	Exon 1 of 4		XP_011514442.1
KLRG2	XM_011516141.3 link	c.605G>A	p.Arg202Gln	missense_variant	Exon 1 of 4		XP_011514443.1
KLRG2	XM_005250311.4 link	c.605G>A	p.Arg202Gln	missense_variant	Exon 1 of 4		XP_005250368.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLRG2	ENST00000340940.5 link	c.605G>A	p.Arg202Gln	missense_variant	Exon 1 of 5	1	NM_198508.4	ENSP00000339356.4		A4D1S0-1
KLRG2	ENST00000393039.2 link	c.605G>A	p.Arg202Gln	missense_variant	Exon 1 of 2	5		ENSP00000376759.2		A4D1S0-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1223242

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

593772

African (AFR)

AF:

0.00

AC:

AN:

23874

American (AMR)

AF:

0.00

AC:

AN:

10040

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17136

East Asian (EAS)

AF:

0.00

AC:

AN:

27370

South Asian (SAS)

AF:

0.00

AC:

AN:

53694

European-Finnish (FIN)

AF:

0.00

AC:

AN:

29818

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3504

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1007338

Other (OTH)

AF:

0.00

AC:

AN:

50468

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000340

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.29

BayesDel_noAF

Benign

-0.65

CADD

Benign

9.0

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.0022

T;.

Eigen

Benign

-0.96

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.033

LIST_S2

Benign

0.65

T;T

M_CAP

Benign

0.0075

MetaRNN

Benign

0.074

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.90

L;L

PhyloP100

-0.083

PrimateAI

Uncertain

0.56

PROVEAN

Benign

-0.49

N;N

REVEL

Benign

0.038

Sift

Benign

0.29

T;T

Sift4G

Benign

0.66

T;T

Polyphen

0.11

B;B

Vest4

0.049

MutPred

0.14

Gain of glycosylation at S204 (P = 0.1176);Gain of glycosylation at S204 (P = 0.1176);

MVP

0.18

MPC

0.93

ClinPred

0.068

GERP RS

1.1

Varity_R

0.026

gMVP

0.069

Mutation Taster

=98/2

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over