rs72481819

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001303618.2(CD226):​c.846G>A​(p.Glu282=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.06 in 1,560,522 control chromosomes in the GnomAD database, including 3,480 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 0.051 ( 301 hom., cov: 32)
Exomes 𝑓: 0.061 ( 3179 hom. )

Consequence

CD226
NM_001303618.2 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.156
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP7
Synonymous conserved (PhyloP=0.156 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0681 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD226NM_001303618.2 linkuse as main transcriptc.846G>A p.Glu282= synonymous_variant 5/6 ENST00000582621.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD226ENST00000582621.6 linkuse as main transcriptc.846G>A p.Glu282= synonymous_variant 5/61 NM_001303618.2 P1

Frequencies

GnomAD3 genomes
AF:
0.0507
AC:
7707
AN:
151980
Hom.:
301
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0159
Gnomad AMI
AF:
0.00548
Gnomad AMR
AF:
0.0427
Gnomad ASJ
AF:
0.0378
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00871
Gnomad FIN
AF:
0.130
Gnomad MID
AF:
0.0256
Gnomad NFE
AF:
0.0697
Gnomad OTH
AF:
0.0470
GnomAD3 exomes
AF:
0.0493
AC:
12359
AN:
250712
Hom.:
501
AF XY:
0.0491
AC XY:
6648
AN XY:
135520
show subpopulations
Gnomad AFR exome
AF:
0.0132
Gnomad AMR exome
AF:
0.0279
Gnomad ASJ exome
AF:
0.0366
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00971
Gnomad FIN exome
AF:
0.120
Gnomad NFE exome
AF:
0.0671
Gnomad OTH exome
AF:
0.0550
GnomAD4 exome
AF:
0.0610
AC:
85856
AN:
1408424
Hom.:
3179
Cov.:
25
AF XY:
0.0595
AC XY:
41903
AN XY:
704000
show subpopulations
Gnomad4 AFR exome
AF:
0.0125
Gnomad4 AMR exome
AF:
0.0304
Gnomad4 ASJ exome
AF:
0.0375
Gnomad4 EAS exome
AF:
0.000127
Gnomad4 SAS exome
AF:
0.00927
Gnomad4 FIN exome
AF:
0.119
Gnomad4 NFE exome
AF:
0.0685
Gnomad4 OTH exome
AF:
0.0537
GnomAD4 genome
AF:
0.0506
AC:
7703
AN:
152098
Hom.:
301
Cov.:
32
AF XY:
0.0532
AC XY:
3954
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.0159
Gnomad4 AMR
AF:
0.0426
Gnomad4 ASJ
AF:
0.0378
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00851
Gnomad4 FIN
AF:
0.130
Gnomad4 NFE
AF:
0.0697
Gnomad4 OTH
AF:
0.0465
Alfa
AF:
0.0566
Hom.:
179
Bravo
AF:
0.0424
Asia WGS
AF:
0.00636
AC:
22
AN:
3474
EpiCase
AF:
0.0602
EpiControl
AF:
0.0603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.3
DANN
Benign
0.23

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs72481819; hg19: chr18-67534632; API