chr7-139458699-C-G

Variant names:

• chr7-139458699-C-G
• rs12113878
• NM_198508.4:c.1006-4485G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_198508.4(KLRG2):​c.1006-4485G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,150 control chromosomes in the GnomAD database, including 4,385 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 0.23 (4385 hom., cov: 32)
• Consequence: KLRG2 NM_198508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 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.1006-4485G>C		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.1006-4485G>C		intron	N/A	ENSP00000339356.4	A4D1S0-1
	KLRG2	ENST00000869133.1		c.1006-4051G>C		intron	N/A	ENSP00000539192.1
	KLRG2	ENST00000941714.1		c.904-4485G>C		intron	N/A	ENSP00000611773.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35692 AN: 152032 Hom.: 4377 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.235 AC: 35739 AN: 152150 Hom.: 4385 Cov.: 32 AF XY: 0.232 AC XY: 17284 AN XY: 74388

African (AFR) AF: 0.270 AC: 11188 AN: 41490

American (AMR) AF: 0.202 AC: 3087 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3470

East Asian (EAS) AF: 0.369 AC: 1914 AN: 5184

South Asian (SAS) AF: 0.286 AC: 1378 AN: 4822

European-Finnish (FIN) AF: 0.145 AC: 1537 AN: 10598

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14972 AN: 67998

Other (OTH) AF: 0.256 AC: 540 AN: 2112

Alfa AF: 0.223 Hom.: 490

Bravo AF: 0.240

Asia WGS AF: 0.319 AC: 1106 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.75
DANN	Benign	0.42
PhyloP100		-1.2
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: rs12113878; hg19: chr7-139143445;