1-160837925-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+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

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=-0.86).
• 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/exons	MANE	UniProt
CD244	NM_016382.4	c.834+526A>G		intron_variant		ENST00000368034.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD244	ENST00000368034.9	c.834+526A>G		intron_variant		1	NM_016382.4	P2

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.568

Gnomad4 OTH AF: 0.583

Alfa AF: 0.571 Hom.: 41355

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

risk factor, no assertion criteria provided

literature only

OMIM

Oct 01, 2008

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.94
Dann	Benign	0.51

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: rs3766379; hg19: chr1-160807715;