7-139478717-A-G

Variant names:

• chr7-139478717-A-G
• rs7779375
• NM_198508.4:c.1005+910T>C

Variant summary

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

The NM_198508.4(KLRG2):​c.1005+910T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,010 control chromosomes in the GnomAD database, including 27,045 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 0.58 (27045 hom., cov: 31)
• Consequence: KLRG2 NM_198508.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KLRG2	NM_198508.4	c.1005+910T>C		intron_variant	Intron 3 of 4	ENST00000340940.5	NP_940910.1
KLRG2	XM_011516140.3	c.1005+910T>C		intron_variant	Intron 3 of 3		XP_011514442.1
KLRG2	XM_011516141.3	c.1005+910T>C		intron_variant	Intron 3 of 3		XP_011514443.1
KLRG2	XM_005250311.4	c.1005+910T>C		intron_variant	Intron 3 of 3		XP_005250368.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KLRG2	ENST00000340940.5	c.1005+910T>C		intron_variant	Intron 3 of 4	1	NM_198508.4	ENSP00000339356.4
KLRG2	ENST00000393039.2	c.757+4169T>C		intron_variant	Intron 1 of 1	5		ENSP00000376759.2

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88107 AN: 151892 Hom.: 26989 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.580 AC: 88217 AN: 152010 Hom.: 27045 Cov.: 31 AF XY: 0.574 AC XY: 42645 AN XY: 74290

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.405

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.607

Alfa AF: 0.511 Hom.: 40090

Bravo AF: 0.596

Asia WGS AF: 0.592 AC: 2054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.61

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: rs7779375; hg19: chr7-139163463;