rs3766379

Variant names:

• chr1-160837925-T-C
• rs3766379
• NM_016382.4:c.834+526A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016382.4(CD244):​c.834+526A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 152,048 control chromosomes in the GnomAD database, including 25,053 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.57 (25053 hom., cov: 32)
• Consequence: CD244 NM_016382.4 intron
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -1.30
• Publications: 22 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=-0.86).
• 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 rank	MANE	Protein	UniProt
CD244	NM_016382.4	c.834+526A>G		intron_variant	Intron 5 of 8	ENST00000368034.9	NP_057466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9	c.834+526A>G		intron_variant	Intron 5 of 8	1	NM_016382.4	ENSP00000357013.4

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86991 AN: 151930 Hom.: 25029 Cov.: 32

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.573 AC: 87067 AN: 152048 Hom.: 25053 Cov.: 32 AF XY: 0.572 AC XY: 42487 AN XY: 74312

African (AFR) AF: 0.576 AC: 23884 AN: 41478

American (AMR) AF: 0.599 AC: 9155 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2251 AN: 3472

East Asian (EAS) AF: 0.460 AC: 2377 AN: 5162

South Asian (SAS) AF: 0.621 AC: 2991 AN: 4816

European-Finnish (FIN) AF: 0.551 AC: 5825 AN: 10570

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38622 AN: 67958

Other (OTH) AF: 0.583 AC: 1230 AN: 2110

Alfa AF: 0.573 Hom.: 55636

Bravo AF: 0.580

Asia WGS AF: 0.536 AC: 1862 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Rheumatoid arthritis Other:1

Oct 01, 2008

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.51
PhyloP100		-1.3
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: rs3766379; hg19: chr1-160807715;