rs1319651

Variant names:

• chr1-160838686-C-A
• rs1319651
• NM_016382.4:c.767-168G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-160838686-C-A
• chr1-160838686-C-G
• chr1-160838686-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_016382.4(CD244):​c.767-168G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 630,590 control chromosomes in the GnomAD database, including 23 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 0.00070 (3 hom., cov: 31)
  • Exomes 𝑓: 0.0021 (20 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=-0.82).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000704 (107/152022) while in subpopulation SAS AF = 0.0209 (101/4822). AF 95% confidence interval is 0.0176. There are 3 homozygotes in GnomAd4. There are 71 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD244	NM_016382.4	c.767-168G>T		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>T		intron_variant	Intron 4 of 8	1	NM_016382.4	ENSP00000357013.4

Frequencies

GnomAD3 genomes AF: 0.000711 AC: 108 AN: 151904 Hom.: 3 Cov.: 31

Gnomad AFR AF: 0.0000484

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.000479

GnomAD4 exome AF: 0.00210 AC: 1006 AN: 478568 Hom.: 20 Cov.: 5 AF XY: 0.00291 AC XY: 741 AN XY: 254686

African (AFR) AF: 0.0000767 AC: 1 AN: 13038

American (AMR) AF: 0.00 AC: 0 AN: 20772

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14428

East Asian (EAS) AF: 0.00 AC: 0 AN: 31694

South Asian (SAS) AF: 0.0198 AC: 940 AN: 47572

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34620

Middle Eastern (MID) AF: 0.00235 AC: 5 AN: 2126

European-Non Finnish (NFE) AF: 0.000101 AC: 29 AN: 287190

Other (OTH) AF: 0.00114 AC: 31 AN: 27128

GnomAD4 genome AF: 0.000704 AC: 107 AN: 152022 Hom.: 3 Cov.: 31 AF XY: 0.000956 AC XY: 71 AN XY: 74292

African (AFR) AF: 0.0000483 AC: 2 AN: 41424

American (AMR) AF: 0.00 AC: 0 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.0209 AC: 101 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10552

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 67986

Other (OTH) AF: 0.000474 AC: 1 AN: 2108

Alfa AF: 0.00 Hom.: 1004

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.054
Mutation Taster		=100/0	polymorphism

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;