7-139453805-C-T

Variant names:

• chr7-139453805-C-T
• rs10954649
• NM_198508.4:c.1110-98G>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.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 NM_198508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 4 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 = 0.665 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.1110-98G>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.1110-98G>A		intron	N/A	ENSP00000339356.4	A4D1S0-1
	KLRG2	ENST00000869133.1		c.1161-98G>A		intron	N/A	ENSP00000539192.1
	KLRG2	ENST00000941714.1		c.1008-98G>A		intron	N/A	ENSP00000611773.1

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64893 AN: 151914 Hom.: 15751 Cov.: 32

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

African (AFR) AF: 0.676 AC: 19795 AN: 29270

American (AMR) AF: 0.292 AC: 10420 AN: 35630

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 9688 AN: 24080

East Asian (EAS) AF: 0.305 AC: 11204 AN: 36686

South Asian (SAS) AF: 0.325 AC: 25204 AN: 77630

European-Finnish (FIN) AF: 0.242 AC: 10797 AN: 44660

Middle Eastern (MID) AF: 0.411 AC: 1862 AN: 4532

European-Non Finnish (NFE) AF: 0.341 AC: 328435 AN: 963376

Other (OTH) AF: 0.368 AC: 19839 AN: 53964

GnomAD4 genome AF: 0.428 AC: 64994 AN: 152032 Hom.: 15797 Cov.: 32 AF XY: 0.418 AC XY: 31069 AN XY: 74326

African (AFR) AF: 0.671 AC: 27824 AN: 41440

American (AMR) AF: 0.345 AC: 5270 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1379 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1650 AN: 5156

South Asian (SAS) AF: 0.339 AC: 1632 AN: 4820

European-Finnish (FIN) AF: 0.230 AC: 2429 AN: 10580

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23511 AN: 67970

Other (OTH) AF: 0.436 AC: 923 AN: 2116

Alfa AF: 0.363 Hom.: 17263

Bravo AF: 0.448

Asia WGS AF: 0.348 AC: 1211 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	0.38
DANN	Benign	0.49
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10954649; hg19: chr7-139138551;