Variant 7-139453805-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000340940.5(KLRG2):c.1110-98G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 1,421,860 control chromosomes in the GnomAD database, including 93,961 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 0.43 ( 15797 hom., cov: 32)

Exomes 𝑓: 0.34 ( 78164 hom. )

Consequence

KLRG2
ENST00000340940.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
KLRG2	NM_198508.4 linkuse as main transcript	c.1110-98G>A	intron_variant	ENST00000340940.5	NP_940910.1
KLRG2	XM_005250311.4 linkuse as main transcript	c.1006-98G>A	intron_variant		XP_005250368.1
KLRG2	XM_011516141.3 linkuse as main transcript	c.1005+25822G>A	intron_variant		XP_011514443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KLRG2	ENST00000340940.5 linkuse as main transcript	c.1110-98G>A		intron_variant		1	NM_198508.4	ENSP00000339356	P1	A4D1S0-1
KLRG2	ENST00000393039.2 linkuse as main transcript	c.758-98G>A		intron_variant		5		ENSP00000376759		A4D1S0-2

Frequencies

GnomAD3 genomes

AF:

0.427

AC:

64893

AN:

151914

Hom.:

15751

Cov.:

show subpopulations

Gnomad AFR

AF:

0.671

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.345

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.319

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.472

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.435

GnomAD4 exome

AF:

0.344

AC:

437244

AN:

1269828

Hom.:

78164

AF XY:

0.343

AC XY:

218284

AN XY:

636180

show subpopulations

Gnomad4 AFR exome

AF:

0.676

Gnomad4 AMR exome

AF:

0.292

Gnomad4 ASJ exome

AF:

0.402

Gnomad4 EAS exome

AF:

0.305

Gnomad4 SAS exome

AF:

0.325

Gnomad4 FIN exome

AF:

0.242

Gnomad4 NFE exome

AF:

0.341

Gnomad4 OTH exome

AF:

0.368

GnomAD4 genome

AF:

0.428

AC:

64994

AN:

152032

Hom.:

15797

Cov.:

AF XY:

0.418

AC XY:

31069

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.671

Gnomad4 AMR

AF:

0.345

Gnomad4 ASJ

AF:

0.398

Gnomad4 EAS

AF:

0.320

Gnomad4 SAS

AF:

0.339

Gnomad4 FIN

AF:

0.230

Gnomad4 NFE

AF:

0.346

Gnomad4 OTH

AF:

0.436

Alfa

AF:

0.351

Hom.:

12473

Bravo

AF:

0.448

Asia WGS

AF:

0.348

AC:

1211

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.38

DANN

Benign

0.49

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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