rs763361
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is . The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
Likely benign
The NM_001303618.2(CD226):c.919A>T(p.Ser307Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,106 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CD226
NM_001303618.2 missense
NM_001303618.2 missense
Scores
19
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0490
Publications
292 publications found
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
new If you want to explore the variant's impact on the transcript NM_001303618.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (REVEL=0.003).
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
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CD226 | MANE Select | c.919A>T | p.Ser307Cys | missense | Exon 6 of 6 | NP_001290547.1 | Q15762 | ||
| CD226 | c.919A>T | p.Ser307Cys | missense | Exon 7 of 7 | NP_006557.2 | Q15762 | |||
| CD226 | c.454A>T | p.Ser152Cys | missense | Exon 5 of 5 | NP_001290548.1 | J3QR77 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| CD226 | TSL:1 MANE Select | c.919A>T | p.Ser307Cys | missense | Exon 6 of 6 | ENSP00000461947.1 | Q15762 | ||
| CD226 | TSL:1 | c.919A>T | p.Ser307Cys | missense | Exon 7 of 7 | ENSP00000280200.4 | Q15762 | ||
| CD226 | TSL:1 | c.454A>T | p.Ser152Cys | missense | Exon 5 of 5 | ENSP00000464084.1 | J3QR77 |
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 151956Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
0
AN:
151956
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
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Gnomad EAS
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Gnomad SAS
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Gnomad FIN
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Gnomad MID
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Gnomad NFE
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251140 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
251140
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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Gnomad NFE exome
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Gnomad OTH exome
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461106Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 726882 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1461106
Hom.:
Cov.:
34
AF XY:
AC XY:
1
AN XY:
726882
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33456
American (AMR)
AF:
AC:
0
AN:
44708
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26114
East Asian (EAS)
AF:
AC:
1
AN:
39634
South Asian (SAS)
AF:
AC:
0
AN:
86222
European-Finnish (FIN)
AF:
AC:
0
AN:
53378
Middle Eastern (MID)
AF:
AC:
0
AN:
5764
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111470
Other (OTH)
AF:
AC:
0
AN:
60360
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome 0.00 AC: 0AN: 151956Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74190
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
151956
Hom.:
Cov.:
32
AF XY:
AC XY:
0
AN XY:
74190
African (AFR)
AF:
AC:
0
AN:
41366
American (AMR)
AF:
AC:
0
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3466
East Asian (EAS)
AF:
AC:
0
AN:
5166
South Asian (SAS)
AF:
AC:
0
AN:
4820
European-Finnish (FIN)
AF:
AC:
0
AN:
10560
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
67980
Other (OTH)
AF:
AC:
0
AN:
2090
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
N
PhyloP100
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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Other links and lift over
dbSNP: rs763361 ;
hg19: chr18-67531642;