Genetic Variant CD244:c.*657A>G (chr1-160830690-T-C) – 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.*657A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,214 control chromosomes in the GnomAD database, including 23,380 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 0.54 ( 23373 hom., cov: 33)

Exomes 𝑓: 0.40 ( 7 hom. )

Consequence

CD244
NM_016382.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.290

Publications

18 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:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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	UniProt
CD244	NM_016382.4	MANE Select	c.*657A>G	3_prime_UTR	Exon 9 of 9	NP_057466.1	Q9BZW8-2
CD244	NM_001166663.2		c.*657A>G	3_prime_UTR	Exon 9 of 9	NP_001160135.1	Q9BZW8-1
CD244	NM_001166664.2		c.*657A>G	3_prime_UTR	Exon 8 of 8	NP_001160136.1	Q9BZW8-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD244	ENST00000368034.9	TSL:1 MANE Select	c.*657A>G		3_prime_UTR	Exon 9 of 9	ENSP00000357013.4	Q9BZW8-2
	CD244	ENST00000884349.1		c.*657A>G		3_prime_UTR	Exon 7 of 7	ENSP00000554408.1

Frequencies

GnomAD3 genomes

AF:

0.545

AC:

82760

AN:

151984

Hom.:

23326

Cov.:

show subpopulations

Gnomad AFR

AF:

0.665

Gnomad AMI

AF:

0.225

Gnomad AMR

AF:

0.611

Gnomad ASJ

AF:

0.544

Gnomad EAS

AF:

0.709

Gnomad SAS

AF:

0.624

Gnomad FIN

AF:

0.484

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.563

GnomAD4 exome

AF:

0.398

AC:

AN:

108

Hom.:

Cov.:

AF XY:

0.424

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.333

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.429

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.545

AC:

82868

AN:

152106

Hom.:

23373

Cov.:

AF XY:

0.548

AC XY:

40733

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.665

AC:

27600

AN:

41494

American (AMR)

AF:

0.612

AC:

9350

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.544

AC:

1887

AN:

3466

East Asian (EAS)

AF:

0.709

AC:

3658

AN:

5160

South Asian (SAS)

AF:

0.626

AC:

3014

AN:

4818

European-Finnish (FIN)

AF:

0.484

AC:

5116

AN:

10574

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.452

AC:

30705

AN:

67988

Other (OTH)

AF:

0.564

AC:

1192

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1924

3847

5771

7694

9618

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

722

1444

2166

2888

3610

<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:

0.486

Hom.:

31202

Bravo

AF:

0.559

Asia WGS

AF:

0.702

AC:

2444

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

7.3

(source)

DANN

Benign

0.69

PhyloP100

0.29

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