rs6945850

Positions:

• chr7-139478872-C-T

Variant summary

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

The NM_198508.4(KLRG2):​c.1005+755G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,556 control chromosomes in the GnomAD database, including 15,362 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 (15362 hom., cov: 30)
• Consequence: KLRG2 NM_198508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

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]

ACMG classification

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 = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLRG2	NM_198508.4	c.1005+755G>A		intron_variant		ENST00000340940.5
KLRG2	XM_005250311.4	c.1005+755G>A		intron_variant
KLRG2	XM_011516140.3	c.1005+755G>A		intron_variant
KLRG2	XM_011516141.3	c.1005+755G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLRG2	ENST00000340940.5	c.1005+755G>A		intron_variant		1	NM_198508.4	P1
KLRG2	ENST00000393039.2	c.757+4014G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65284 AN: 151438 Hom.: 15330 Cov.: 30

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.431 AC: 65376 AN: 151556 Hom.: 15362 Cov.: 30 AF XY: 0.425 AC XY: 31495 AN XY: 74046

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.342

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.447

Alfa AF: 0.372 Hom.: 19092

Bravo AF: 0.445

Asia WGS AF: 0.367 AC: 1277 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	5.1
DANN	Benign	0.65

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

Other links and lift over

dbSNP: rs6945850; hg19: chr7-139163618;