rs12036670

Variant names:

• chr1-160863071-A-G
• rs12036670
• NM_016382.4:c.-394T>C

Variant summary

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

The NM_016382.4(CD244):​c.-394T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,088 control chromosomes in the GnomAD database, including 6,165 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 0.27 (6165 hom., cov: 32)
• Consequence: CD244 NM_016382.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD244	NM_016382.4	c.-394T>C		upstream_gene_variant		ENST00000368034.9	NP_057466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9	c.-394T>C		upstream_gene_variant		1	NM_016382.4	ENSP00000357013.4

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40722 AN: 151970 Hom.: 6154 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.268 AC: 40779 AN: 152088 Hom.: 6165 Cov.: 32 AF XY: 0.269 AC XY: 19979 AN XY: 74348

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.252

Alfa AF: 0.241 Hom.: 809

Bravo AF: 0.273

Asia WGS AF: 0.397 AC: 1382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.7
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12036670; hg19: chr1-160832861;