dbSNP rs6682654: CD244:c.656-164C>T (chr1-160839213-G-A) – 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.656-164C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 582,304 control chromosomes in the GnomAD database, including 79,663 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 0.45 ( 17534 hom., cov: 32)

Exomes 𝑓: 0.53 ( 62129 hom. )

Consequence

CD244
NM_016382.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.939

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=-0.79).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016382.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD244	NM_016382.4	MANE Select	c.656-164C>T	intron	N/A	NP_057466.1
CD244	NM_001166663.2		c.671-164C>T	intron	N/A	NP_001160135.1
CD244	NM_001166664.2		c.380-164C>T	intron	N/A	NP_001160136.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD244	ENST00000368034.9	TSL:1 MANE Select	c.656-164C>T	intron	N/A	ENSP00000357013.4
CD244	ENST00000368033.7	TSL:1	c.671-164C>T	intron	N/A	ENSP00000357012.3
CD244	ENST00000322302.7	TSL:1	c.380-164C>T	intron	N/A	ENSP00000313619.7

Frequencies

GnomAD3 genomes

AF:

0.453

AC:

68774

AN:

151876

Hom.:

17530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.202

Gnomad AMI

AF:

0.593

Gnomad AMR

AF:

0.545

Gnomad ASJ

AF:

0.595

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.481

Gnomad FIN

AF:

0.547

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.560

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.531

AC:

228681

AN:

430310

Hom.:

62129

Cov.:

AF XY:

0.532

AC XY:

121275

AN XY:

228158

show subpopulations

African (AFR)

AF:

0.212

AC:

2500

AN:

11796

American (AMR)

AF:

0.594

AC:

9872

AN:

16632

Ashkenazi Jewish (ASJ)

AF:

0.582

AC:

7502

AN:

12888

East Asian (EAS)

AF:

0.395

AC:

11444

AN:

28942

South Asian (SAS)

AF:

0.494

AC:

21566

AN:

43666

European-Finnish (FIN)

AF:

0.554

AC:

16599

AN:

29980

Middle Eastern (MID)

AF:

0.574

AC:

1511

AN:

2632

European-Non Finnish (NFE)

AF:

0.559

AC:

144928

AN:

259088

Other (OTH)

AF:

0.517

AC:

12759

AN:

24686

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

4800

9600

14401

19201

24001

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

674

1348

2022

2696

3370

<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:

0.453

AC:

68791

AN:

151994

Hom.:

17534

Cov.:

AF XY:

0.452

AC XY:

33563

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.202

AC:

8377

AN:

41454

American (AMR)

AF:

0.546

AC:

8335

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.595

AC:

2060

AN:

3464

East Asian (EAS)

AF:

0.410

AC:

2114

AN:

5154

South Asian (SAS)

AF:

0.482

AC:

2324

AN:

4826

European-Finnish (FIN)

AF:

0.547

AC:

5778

AN:

10556

Middle Eastern (MID)

AF:

0.571

AC:

168

AN:

294

European-Non Finnish (NFE)

AF:

0.560

AC:

38065

AN:

67966

Other (OTH)

AF:

0.491

AC:

1034

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1755

3510

5266

7021

8776

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.514

Hom.:

8945

Bravo

AF:

0.447

Asia WGS

AF:

0.411

AC:

1430

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

8.9

(source)

DANN

Benign

0.70

PhyloP100

0.94

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over