18-69958049-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000579496.5(CD226):​c.-127+3543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,008 control chromosomes in the GnomAD database, including 18,736 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 ( 18736 hom., cov: 31)

Consequence

CD226
ENST00000579496.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.63
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CD226XM_006722374.4 linkc.13+3543G>A intron_variant XP_006722437.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD226ENST00000579496.5 linkc.-127+3543G>A intron_variant 5 ENSP00000463927.1 J3QQW1

Frequencies

GnomAD3 genomes
AF:
0.449
AC:
68134
AN:
151890
Hom.:
18723
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.113
Gnomad AMI
AF:
0.423
Gnomad AMR
AF:
0.538
Gnomad ASJ
AF:
0.569
Gnomad EAS
AF:
0.597
Gnomad SAS
AF:
0.563
Gnomad FIN
AF:
0.667
Gnomad MID
AF:
0.373
Gnomad NFE
AF:
0.574
Gnomad OTH
AF:
0.444
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.448
AC:
68157
AN:
152008
Hom.:
18736
Cov.:
31
AF XY:
0.456
AC XY:
33850
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.112
Gnomad4 AMR
AF:
0.539
Gnomad4 ASJ
AF:
0.569
Gnomad4 EAS
AF:
0.598
Gnomad4 SAS
AF:
0.563
Gnomad4 FIN
AF:
0.667
Gnomad4 NFE
AF:
0.574
Gnomad4 OTH
AF:
0.449
Alfa
AF:
0.549
Hom.:
30652
Bravo
AF:
0.425
Asia WGS
AF:
0.562
AC:
1949
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
0.33
DANN
Benign
0.82

Splicing

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: rs1539964; hg19: chr18-67625285; API