Genetic Variant CD244:c.960+39T>C (chr1-160834012-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016382.4(CD244):c.960+39T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 1,467,252 control chromosomes in the GnomAD database, including 262,992 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 0.53 ( 22642 hom., cov: 32)

Exomes 𝑓: 0.60 ( 240350 hom. )

Consequence

CD244
NM_016382.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.307

Publications

17 publications found

Variant links:

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]

CD244 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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 = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD244	NM_016382.4 link	c.960+39T>C		intron_variant	Intron 7 of 8	ENST00000368034.9	NP_057466.1	Q9BZW8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9 link	c.960+39T>C		intron_variant	Intron 7 of 8	1	NM_016382.4	ENSP00000357013.4		Q9BZW8-2

Frequencies

GnomAD3 genomes

AF:

0.534

AC:

81115

AN:

151918

Hom.:

22633

Cov.:

show subpopulations

Gnomad AFR

AF:

0.362

Gnomad AMI

AF:

0.591

Gnomad AMR

AF:

0.592

Gnomad ASJ

AF:

0.669

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.600

Gnomad FIN

AF:

0.601

Gnomad MID

AF:

0.655

Gnomad NFE

AF:

0.606

Gnomad OTH

AF:

0.565

GnomAD2 exomes

AF:

0.593

AC:

148268

AN:

250096

AF XY:

0.596

show subpopulations

Gnomad AFR exome

AF:

0.360

Gnomad AMR exome

AF:

0.663

Gnomad ASJ exome

AF:

0.660

Gnomad EAS exome

AF:

0.498

Gnomad FIN exome

AF:

0.606

Gnomad NFE exome

AF:

0.608

Gnomad OTH exome

AF:

0.600

GnomAD4 exome

AF:

0.601

AC:

791088

AN:

1315216

Hom.:

240350

Cov.:

AF XY:

0.603

AC XY:

398950

AN XY:

662078

show subpopulations

African (AFR)

AF:

0.368

AC:

11173

AN:

30380

American (AMR)

AF:

0.655

AC:

29073

AN:

44380

Ashkenazi Jewish (ASJ)

AF:

0.661

AC:

16659

AN:

25210

East Asian (EAS)

AF:

0.465

AC:

18119

AN:

38976

South Asian (SAS)

AF:

0.605

AC:

50233

AN:

83076

European-Finnish (FIN)

AF:

0.604

AC:

32189

AN:

53270

Middle Eastern (MID)

AF:

0.641

AC:

3500

AN:

5458

European-Non Finnish (NFE)

AF:

0.611

AC:

597795

AN:

978978

Other (OTH)

AF:

0.583

AC:

32347

AN:

55488

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

14853

29705

44558

59410

74263

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15244

30488

45732

60976

76220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.534

AC:

81154

AN:

152036

Hom.:

22642

Cov.:

AF XY:

0.535

AC XY:

39723

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.362

AC:

15019

AN:

41452

American (AMR)

AF:

0.592

AC:

9056

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.669

AC:

2319

AN:

3466

East Asian (EAS)

AF:

0.467

AC:

2415

AN:

5172

South Asian (SAS)

AF:

0.601

AC:

2891

AN:

4812

European-Finnish (FIN)

AF:

0.601

AC:

6346

AN:

10566

Middle Eastern (MID)

AF:

0.656

AC:

193

AN:

294

European-Non Finnish (NFE)

AF:

0.606

AC:

41192

AN:

67968

Other (OTH)

AF:

0.562

AC:

1184

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1876

3752

5627

7503

9379

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

702

1404

2106

2808

3510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.587

Hom.:

35813

Bravo

AF:

0.531

Asia WGS

AF:

0.501

AC:

1740

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.57

(source)

DANN

Benign

0.58

PhyloP100

-0.31

Mutation Taster

=15/85

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over