rs3809214

Variant names:

• chr12-10306970-G-A
• rs3809214
• ENST00000381908.7:c.-100-1008G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-10306970-G-A
• chr12-10306970-G-C

Variant summary

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

The NM_001351060.2(KLRD1):​c.-100-1008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.559 in 151,936 control chromosomes in the GnomAD database, including 24,641 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 0.56 (24641 hom., cov: 32)
• Consequence: KLRD1 NM_001351060.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 5 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001351060.2. 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
	KLRD1	NM_001351060.2		c.-100-1008G>A		intron	N/A	NP_001337989.1
	KLRD1	NM_001114396.3		c.-100-1008G>A		intron	N/A	NP_001107868.2	Q13241-1
	KLRD1	NM_001351062.2		c.-101+738G>A		intron	N/A	NP_001337991.1	Q13241-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRD1	ENST00000381908.7	TSL:1	c.-100-1008G>A		intron	N/A	ENSP00000371333.4	Q13241-1
	KLRD1	ENST00000540271.1	TSL:1	n.251-1008G>A		intron	N/A
	KLRD1	ENST00000862987.1		c.-101+738G>A		intron	N/A	ENSP00000533046.1

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84942 AN: 151818 Hom.: 24636 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.643

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.559 AC: 84970 AN: 151936 Hom.: 24641 Cov.: 32 AF XY: 0.558 AC XY: 41413 AN XY: 74240

African (AFR) AF: 0.396 AC: 16389 AN: 41416

American (AMR) AF: 0.571 AC: 8720 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2333 AN: 3472

East Asian (EAS) AF: 0.449 AC: 2322 AN: 5166

South Asian (SAS) AF: 0.668 AC: 3220 AN: 4818

European-Finnish (FIN) AF: 0.586 AC: 6165 AN: 10514

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.643 AC: 43671 AN: 67960

Other (OTH) AF: 0.598 AC: 1261 AN: 2108

Alfa AF: 0.616 Hom.: 110020

Bravo AF: 0.550

Asia WGS AF: 0.558 AC: 1938 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.19
DANN	Benign	0.59
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

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

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

Other links and lift over

dbSNP: rs3809214;

hg19: chr12-10459569;