dbSNP rs34794968: CD226:c.*524G>T (chr18-69863790-C-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_001303618.2(CD226):c.*524G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,456 control chromosomes in the GnomAD database, including 10,044 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 0.36 ( 9992 hom., cov: 32)

Exomes 𝑓: 0.42 ( 52 hom. )

Consequence

CD226
NM_001303618.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

19 publications found

Variant links:

Genes affected

CD226 (HGNC:16961): (CD226 molecule) This gene encodes a glycoprotein expressed on the surface of NK cells, platelets, monocytes and a subset of T cells. It is a member of the Ig-superfamily containing 2 Ig-like domains of the V-set. The protein mediates cellular adhesion of platelets and megakaryocytic cells to vascular endothelial cells. The protein also plays a role in megakaryocytic cell maturation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]

CD226 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001303618.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD226	NM_001303618.2	MANE Select	c.*524G>T	3_prime_UTR	Exon 6 of 6	NP_001290547.1	Q15762
CD226	NM_006566.4		c.*524G>T	3_prime_UTR	Exon 7 of 7	NP_006557.2	Q15762
CD226	NM_001303619.2		c.*524G>T	3_prime_UTR	Exon 5 of 5	NP_001290548.1	J3QR77

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD226	ENST00000582621.6	TSL:1 MANE Select	c.*524G>T	3_prime_UTR	Exon 6 of 6	ENSP00000461947.1	Q15762
CD226	ENST00000280200.8	TSL:1	c.*524G>T	3_prime_UTR	Exon 7 of 7	ENSP00000280200.4	Q15762
CD226	ENST00000581982.5	TSL:1	c.*524G>T	3_prime_UTR	Exon 5 of 5	ENSP00000464084.1	J3QR77

Frequencies

GnomAD3 genomes

AF:

0.357

AC:

54276

AN:

151890

Hom.:

9981

Cov.:

show subpopulations

Gnomad AFR

AF:

0.312

Gnomad AMI

AF:

0.482

Gnomad AMR

AF:

0.342

Gnomad ASJ

AF:

0.373

Gnomad EAS

AF:

0.243

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.487

Gnomad NFE

AF:

0.399

Gnomad OTH

AF:

0.390

GnomAD4 exome

AF:

0.424

AC:

190

AN:

448

Hom.:

Cov.:

AF XY:

0.443

AC XY:

108

AN XY:

244

show subpopulations

African (AFR)

AF:

0.833

AC:

AN:

American (AMR)

AF:

0.385

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

0.167

AC:

AN:

South Asian (SAS)

AF:

0.833

AC:

AN:

European-Finnish (FIN)

AF:

0.333

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.414

AC:

158

AN:

382

Other (OTH)

AF:

0.167

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

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:

0.357

AC:

54324

AN:

152008

Hom.:

9992

Cov.:

AF XY:

0.352

AC XY:

26164

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.312

AC:

12942

AN:

41458

American (AMR)

AF:

0.343

AC:

5234

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.373

AC:

1294

AN:

3470

East Asian (EAS)

AF:

0.242

AC:

1252

AN:

5174

South Asian (SAS)

AF:

0.408

AC:

1964

AN:

4818

European-Finnish (FIN)

AF:

0.295

AC:

3112

AN:

10554

Middle Eastern (MID)

AF:

0.480

AC:

141

AN:

294

European-Non Finnish (NFE)

AF:

0.399

AC:

27119

AN:

67944

Other (OTH)

AF:

0.391

AC:

826

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1766

3532

5298

7064

8830

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

546

1092

1638

2184

2730

<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:

0.381

Hom.:

3946

Bravo

AF:

0.362

Asia WGS

AF:

0.316

AC:

1102

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.34

(source)

DANN

Benign

0.36

PhyloP100

-1.8

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

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over