rs12829155

Variant names:

• chr12-10315655-A-G
• rs12829155
• NM_002262.5:c.*862A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-10315655-A-G
• chr12-10315655-A-T

Variant summary

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

The NM_002262.5(KLRD1):​c.*862A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,882 control chromosomes in the GnomAD database, including 19,908 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 0.49 (19908 hom., cov: 31)
  • Exomes 𝑓: 0.68 (63 hom.)
  • Failed GnomAD Quality Control
• Consequence: KLRD1 NM_002262.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002262.5. 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_002262.5	MANE Select	c.*862A>G		3_prime_UTR	Exon 6 of 6	NP_002253.2
	KLRD1	NR_147038.2		n.1614A>G		non_coding_transcript_exon	Exon 6 of 6
	KLRD1	NR_147039.2		n.1560A>G		non_coding_transcript_exon	Exon 6 of 6

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KLRD1	ENST00000336164.9	TSL:1 MANE Select	c.*862A>G		3_prime_UTR	Exon 6 of 6	ENSP00000338130.4
	KLRD1	ENST00000381908.7	TSL:1	c.*862A>G		3_prime_UTR	Exon 7 of 7	ENSP00000371333.4
	KLRD1	ENST00000350274.9	TSL:1	c.*862A>G		3_prime_UTR	Exon 5 of 5	ENSP00000310929.7

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73788 AN: 151764 Hom.: 19910 Cov.: 31

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.507

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.680 AC: 193 AN: 284 Hom.: 63 Cov.: 0 AF XY: 0.652 AC XY: 116 AN XY: 178

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.700 AC: 7 AN: 10

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AF: 0.944 AC: 17 AN: 18

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.674 AC: 155 AN: 230

Other (OTH) AF: 0.500 AC: 7 AN: 14

GnomAD4 genome AF: 0.486 AC: 73788 AN: 151882 Hom.: 19908 Cov.: 31 AF XY: 0.487 AC XY: 36110 AN XY: 74218

African (AFR) AF: 0.241 AC: 9977 AN: 41404

American (AMR) AF: 0.492 AC: 7505 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2039 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2259 AN: 5172

South Asian (SAS) AF: 0.671 AC: 3228 AN: 4812

European-Finnish (FIN) AF: 0.562 AC: 5907 AN: 10506

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.603 AC: 40947 AN: 67954

Other (OTH) AF: 0.510 AC: 1076 AN: 2108

Alfa AF: 0.434 Hom.: 1419

Bravo AF: 0.468

Asia WGS AF: 0.548 AC: 1903 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.49
PhyloP100		0.16
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

Other links and lift over

dbSNP: rs12829155; hg19: chr12-10468254;