rs11265493

Variant names:

• chr1-160834012-A-G
• rs11265493
• NM_016382.4:c.960+39T>C

Variant summary

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

The NM_016382.4(CD244):​c.960+39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 1,467,252 control chromosomes in the GnomAD database, including 262,992 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 0.53 (22642 hom., cov: 32)
  • Exomes 𝑓: 0.60 (240350 hom.)
• Consequence: CD244 NM_016382.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 17 publications found

Genes affected

CD244 (HGNC:18171): (CD244 molecule) This gene encodes a cell surface receptor expressed on natural killer (NK) cells (and some T cells) that mediate non-major histocompatibility complex (MHC) restricted killing. The interaction between NK-cell and target cells via this receptor is thought to modulate NK-cell cytolytic activity. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016382.4. 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
	CD244	NM_016382.4	MANE Select	c.960+39T>C		intron	N/A	NP_057466.1
	CD244	NM_001166663.2		c.975+39T>C		intron	N/A	NP_001160135.1
	CD244	NM_001166664.2		c.684+39T>C		intron	N/A	NP_001160136.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD244	ENST00000368034.9	TSL:1 MANE Select	c.960+39T>C		intron	N/A	ENSP00000357013.4
	CD244	ENST00000368033.7	TSL:1	c.975+39T>C		intron	N/A	ENSP00000357012.3
	CD244	ENST00000322302.7	TSL:1	c.684+39T>C		intron	N/A	ENSP00000313619.7

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81115 AN: 151918 Hom.: 22633 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.565

GnomAD2 exomes AF: 0.593 AC: 148268 AN: 250096 AF XY: 0.596

Gnomad AFR exome AF: 0.360

Gnomad AMR exome AF: 0.663

Gnomad ASJ exome AF: 0.660

Gnomad EAS exome AF: 0.498

Gnomad FIN exome AF: 0.606

Gnomad NFE exome AF: 0.608

Gnomad OTH exome AF: 0.600

GnomAD4 exome AF: 0.601 AC: 791088 AN: 1315216 Hom.: 240350 Cov.: 19 AF XY: 0.603 AC XY: 398950 AN XY: 662078

African (AFR) AF: 0.368 AC: 11173 AN: 30380

American (AMR) AF: 0.655 AC: 29073 AN: 44380

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 16659 AN: 25210

East Asian (EAS) AF: 0.465 AC: 18119 AN: 38976

South Asian (SAS) AF: 0.605 AC: 50233 AN: 83076

European-Finnish (FIN) AF: 0.604 AC: 32189 AN: 53270

Middle Eastern (MID) AF: 0.641 AC: 3500 AN: 5458

European-Non Finnish (NFE) AF: 0.611 AC: 597795 AN: 978978

Other (OTH) AF: 0.583 AC: 32347 AN: 55488

GnomAD4 genome AF: 0.534 AC: 81154 AN: 152036 Hom.: 22642 Cov.: 32 AF XY: 0.535 AC XY: 39723 AN XY: 74314

African (AFR) AF: 0.362 AC: 15019 AN: 41452

American (AMR) AF: 0.592 AC: 9056 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2319 AN: 3466

East Asian (EAS) AF: 0.467 AC: 2415 AN: 5172

South Asian (SAS) AF: 0.601 AC: 2891 AN: 4812

European-Finnish (FIN) AF: 0.601 AC: 6346 AN: 10566

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41192 AN: 67968

Other (OTH) AF: 0.562 AC: 1184 AN: 2108

Alfa AF: 0.587 Hom.: 35813

Bravo AF: 0.531

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.57
DANN	Benign	0.58
PhyloP100		-0.31
Mutation Taster		=15/85	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11265493; hg19: chr1-160803802; COSMIC: COSV59237800;