rs6945850

Variant names:

• chr7-139478872-C-T
• rs6945850
• NM_198508.4:c.1005+755G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198508.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRG2	NM_198508.4	MANE Select	c.1005+755G>A		intron	N/A	NP_940910.1	A4D1S0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRG2	ENST00000340940.5	TSL:1 MANE Select	c.1005+755G>A		intron	N/A	ENSP00000339356.4	A4D1S0-1
	KLRG2	ENST00000869133.1		c.1005+755G>A		intron	N/A	ENSP00000539192.1
	KLRG2	ENST00000941714.1		c.903+755G>A		intron	N/A	ENSP00000611773.1

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

African (AFR) AF: 0.635 AC: 26177 AN: 41242

American (AMR) AF: 0.351 AC: 5336 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3472

East Asian (EAS) AF: 0.392 AC: 2002 AN: 5110

South Asian (SAS) AF: 0.342 AC: 1645 AN: 4808

European-Finnish (FIN) AF: 0.295 AC: 3096 AN: 10512

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.361 AC: 24511 AN: 67886

Other (OTH) AF: 0.447 AC: 939 AN: 2100

Alfa AF: 0.384 Hom.: 47749

Bravo AF: 0.445

Asia WGS AF: 0.367 AC: 1277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.65
PhyloP100		0.099
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6945850; hg19: chr7-139163618;