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GeneBe

rs763361

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_001303618.2(CD226):c.919A>T(p.Ser307Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S307G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000040 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CD226
NM_001303618.2 missense

Scores

18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0490

Links

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
?
Computational evidence support a benign effect (MetaRNN=0.075356126).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD226NM_001303618.2 linkuse as main transcriptc.919A>T p.Ser307Cys missense_variant 6/6 ENST00000582621.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD226ENST00000582621.6 linkuse as main transcriptc.919A>T p.Ser307Cys missense_variant 6/61 NM_001303618.2 P1

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
151956
Hom.:
0
Cov.:
32
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251140
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135744
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461106
Hom.:
0
AF XY:
0.00000138
AC XY:
1
AN XY:
726882
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.10
BayesDel_addAF
Benign
-0.35
T
BayesDel_noAF
Benign
-0.58
Cadd
Benign
9.4
Dann
Benign
0.48
DEOGEN2
Benign
0.067
T;T;T;T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.023
N
M_CAP
Benign
0.0057
T
MetaRNN
Benign
0.075
T;T;T;T
MetaSVM
Benign
-0.99
T
MutationAssessor
Benign
0.69
N;.;.;N
MutationTaster
Benign
1.0
P;P;P;P
PrimateAI
Benign
0.28
T
PROVEAN
Benign
-0.89
N;.;.;.
REVEL
Benign
0.0030
Sift
Benign
0.11
T;.;.;.
Sift4G
Benign
0.082
T;T;T;T
Polyphen
0.19
B;.;.;B
Vest4
0.14
MutPred
0.16
Loss of glycosylation at S307 (P = 0.018);.;.;Loss of glycosylation at S307 (P = 0.018);
MVP
0.43
MPC
0.26
ClinPred
0.062
T
GERP RS
0.23
Varity_R
0.065
gMVP
0.22

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.080
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: rs763361; hg19: chr18-67531642; API