rs2900385

chr12-10239017-G-Achr12-10239017-G-Cchr12-10239017-G-T

Variant summary

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

The ENST00000540271.1(KLRD1):n.168+12784G>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KLRD1	NM_001351060.2	c.-1426G>A		5_prime_UTR_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KLRD1	ENST00000540271.1	n.168+12784G>A		intron_variant, non_coding_transcript_variant		1
KLRD1	ENST00000544747.5	c.-101+12784G>A		intron_variant		3

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

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.945

Gnomad4 EAS AF: 0.853

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.993

Gnomad4 NFE AF: 0.978

Gnomad4 OTH AF: 0.892

Alfa AF: 0.956 Hom.: 84871

Bravo AF: 0.867

Asia WGS AF: 0.848 AC: 2945 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.038
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2900385; hg19: chr12-10391616;