1-160837363-T-C

Variant summary

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

The NM_016382.4(CD244):c.834+1088A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.581 in 152,068 control chromosomes in the GnomAD database, including 25,793 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 0.58 (25793 hom., cov: 32)
• Consequence: CD244 NM_016382.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD244	NM_016382.4	c.834+1088A>G		intron_variant		ENST00000368034.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD244	ENST00000368034.9	c.834+1088A>G		intron_variant		1	NM_016382.4	P2

Frequencies

GnomAD3 genomes AF: 0.581 AC: 88218 AN: 151950 Hom.: 25770 Cov.: 32

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.581 AC: 88293 AN: 152068 Hom.: 25793 Cov.: 32 AF XY: 0.580 AC XY: 43092 AN XY: 74318

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.647

Gnomad4 EAS AF: 0.459

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.584

Alfa AF: 0.577 Hom.: 12911

Bravo AF: 0.589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.6
Dann	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs3753389; hg19: chr1-160807153;