1-160838686-C-G

Position:

• chr1-160838686-C-G

Variant summary

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

The NM_016382.4(CD244):​c.767-168G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.525 in 630,148 control chromosomes in the GnomAD database, including 89,424 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 0.48 (18609 hom., cov: 31)
  • Exomes 𝑓: 0.54 (70815 hom.)
• Consequence: CD244 NM_016382.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540

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 = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD244	NM_016382.4	c.767-168G>C		intron_variant		ENST00000368034.9	NP_057466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9	c.767-168G>C		intron_variant		1	NM_016382.4	ENSP00000357013.4

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72632 AN: 151856 Hom.: 18601 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.539 AC: 257956 AN: 478174 Hom.: 70815 Cov.: 5 AF XY: 0.540 AC XY: 137508 AN XY: 254440

Gnomad4 AFR exome AF: 0.288

Gnomad4 AMR exome AF: 0.605

Gnomad4 ASJ exome AF: 0.604

Gnomad4 EAS exome AF: 0.399

Gnomad4 SAS exome AF: 0.516

Gnomad4 FIN exome AF: 0.556

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.528

GnomAD4 genome AF: 0.478 AC: 72669 AN: 151974 Hom.: 18609 Cov.: 31 AF XY: 0.477 AC XY: 35420 AN XY: 74268

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.514

Alfa AF: 0.369 Hom.: 1004

Bravo AF: 0.477

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.35

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: rs1319651; hg19: chr1-160808476;