chr12-10239017-G-A

Variant names:

• chr12-10239017-G-A
• rs2900385
• ENST00000540271.1:n.168+12784G>A

Variant summary

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

The ENST00000540271.1(KLRD1):​n.168+12784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.88 in 152,202 control chromosomes in the GnomAD database, including 60,328 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 0.88 (60328 hom., cov: 32)
• Consequence: KLRD1 ENST00000540271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

Genes affected

KLRD1 (HGNC:6378): (killer cell lectin like receptor D1) Natural killer (NK) cells are a distinct lineage of lymphocytes that mediate cytotoxic activity and secrete cytokines upon immune stimulation. Several genes of the C-type lectin superfamily, including members of the NKG2 family, are expressed by NK cells and may be involved in the regulation of NK cell function. KLRD1 (CD94) is an antigen preferentially expressed on NK cells and is classified as a type II membrane protein because it has an external C terminus. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2017]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540271.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRD1	NM_001351060.2		c.-1426G>A		5_prime_UTR	Exon 1 of 9	NP_001337989.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRD1	ENST00000540271.1	TSL:1	n.168+12784G>A		intron	N/A
	KLRD1	ENST00000544747.5	TSL:3	c.-101+12784G>A		intron	N/A	ENSP00000438669.1

Frequencies

GnomAD3 genomes AF: 0.880 AC: 133857 AN: 152084 Hom.: 60311 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.991

Gnomad AMR AF: 0.936

Gnomad ASJ AF: 0.945

Gnomad EAS AF: 0.853

Gnomad SAS AF: 0.862

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.978

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.880 AC: 133924 AN: 152202 Hom.: 60328 Cov.: 32 AF XY: 0.883 AC XY: 65719 AN XY: 74426

African (AFR) AF: 0.666 AC: 27611 AN: 41450

American (AMR) AF: 0.937 AC: 14321 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.945 AC: 3281 AN: 3472

East Asian (EAS) AF: 0.853 AC: 4420 AN: 5184

South Asian (SAS) AF: 0.862 AC: 4163 AN: 4828

European-Finnish (FIN) AF: 0.993 AC: 10541 AN: 10616

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.978 AC: 66515 AN: 68042

Other (OTH) AF: 0.892 AC: 1886 AN: 2114

Alfa AF: 0.942 Hom.: 195745

Bravo AF: 0.867

Asia WGS AF: 0.848 AC: 2945 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.038
DANN	Benign	0.81
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2900385; hg19: chr12-10391616;