1-160838686-C-G

Variant names:

• chr1-160838686-C-G
• rs1319651
• NM_016382.4:c.767-168G>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.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
• Publications: 5 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 = 0.558 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD244	NM_016382.4	c.767-168G>C		intron_variant	Intron 4 of 8	ENST00000368034.9	NP_057466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9	c.767-168G>C		intron_variant	Intron 4 of 8	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

African (AFR) AF: 0.288 AC: 3758 AN: 13032

American (AMR) AF: 0.605 AC: 12563 AN: 20760

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 8714 AN: 14418

East Asian (EAS) AF: 0.399 AC: 12626 AN: 31678

South Asian (SAS) AF: 0.516 AC: 24512 AN: 47530

European-Finnish (FIN) AF: 0.556 AC: 19237 AN: 34588

Middle Eastern (MID) AF: 0.590 AC: 1253 AN: 2124

European-Non Finnish (NFE) AF: 0.561 AC: 160969 AN: 286940

Other (OTH) AF: 0.528 AC: 14324 AN: 27104

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

African (AFR) AF: 0.281 AC: 11634 AN: 41414

American (AMR) AF: 0.557 AC: 8526 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2141 AN: 3468

East Asian (EAS) AF: 0.415 AC: 2138 AN: 5150

South Asian (SAS) AF: 0.505 AC: 2434 AN: 4818

European-Finnish (FIN) AF: 0.547 AC: 5768 AN: 10544

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38232 AN: 67970

Other (OTH) AF: 0.514 AC: 1083 AN: 2108

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
PhyloP100		-0.054
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1319651; hg19: chr1-160808476;