NM_016382.4:c.960+39T>C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD244	NM_016382.4	c.960+39T>C		intron_variant	Intron 7 of 8	ENST00000368034.9	NP_057466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9	c.960+39T>C		intron_variant	Intron 7 of 8	1	NM_016382.4	ENSP00000357013.4

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

GnomAD3 exomes AF: 0.593 AC: 148268 AN: 250096 Hom.: 44693 AF XY: 0.596 AC XY: 80563 AN XY: 135198

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 SAS exome AF: 0.603

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

Gnomad4 AFR exome AF: 0.368

Gnomad4 AMR exome AF: 0.655

Gnomad4 ASJ exome AF: 0.661

Gnomad4 EAS exome AF: 0.465

Gnomad4 SAS exome AF: 0.605

Gnomad4 FIN exome AF: 0.604

Gnomad4 NFE exome AF: 0.611

Gnomad4 OTH exome AF: 0.583

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

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.467

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.601

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.562

Alfa AF: 0.596 Hom.: 29388

Bravo AF: 0.531

Asia WGS AF: 0.501 AC: 1740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.57
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs11265493; hg19: chr1-160803802; COSMIC: COSV59237800;