12-9126085-A-G

Variant names:

• chr12-9126085-A-G
• rs7305636
• XM_017018684.2:c.*34-9001A>G

Variant summary

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

The ENST00000839050.1(ENSG00000309149):​n.80+649A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 152,128 control chromosomes in the GnomAD database, including 5,675 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 0.26 (5675 hom., cov: 33)
• Consequence: ENSG00000309149 ENST00000839050.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 4 publications found

Genes affected

KLRG1 (HGNC:6380): (killer cell lectin like receptor G1) Natural killer (NK) cells are lymphocytes that can mediate lysis of certain tumor cells and virus-infected cells without previous activation. They can also regulate specific humoral and cell-mediated immunity. The protein encoded by this gene belongs to the killer cell lectin-like receptor (KLR) family, which is a group of transmembrane proteins preferentially expressed in NK cells. Studies in mice suggested that the expression of this gene may be regulated by MHC class I molecules. [provided by RefSeq, Jun 2016]

ENSG00000309149 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839050.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309149	ENST00000839050.1		n.80+649A>G		intron	N/A
	ENSG00000309149	ENST00000839052.1		n.448+649A>G		intron	N/A
	ENSG00000309200	ENST00000839522.1		n.492-642T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38920 AN: 152010 Hom.: 5670 Cov.: 33

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.256 AC: 38947 AN: 152128 Hom.: 5675 Cov.: 33 AF XY: 0.258 AC XY: 19159 AN XY: 74376

African (AFR) AF: 0.134 AC: 5563 AN: 41504

American (AMR) AF: 0.335 AC: 5115 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 779 AN: 3472

East Asian (EAS) AF: 0.0642 AC: 333 AN: 5188

South Asian (SAS) AF: 0.207 AC: 999 AN: 4828

European-Finnish (FIN) AF: 0.358 AC: 3776 AN: 10552

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.317 AC: 21547 AN: 67986

Other (OTH) AF: 0.251 AC: 530 AN: 2110

Alfa AF: 0.297 Hom.: 908

Bravo AF: 0.247

Asia WGS AF: 0.155 AC: 540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.3
DANN	Benign	0.52
PhyloP100		0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7305636;

hg19: chr12-9278681;