11-118349027-G-A

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS1

The NM_000073.3(CD3G):​c.56G>A​(p.Gly19Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00118 in 1,614,066 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00070 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 1 hom. )

Consequence

CD3G
NM_000073.3 missense, splice_region

Scores

1
10
8
Splicing: ADA: 0.7647
2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:2

Conservation

PhyloP100: 2.72
Variant links:
Genes affected
CD3G (HGNC:1675): (CD3 gamma subunit of T-cell receptor complex) The protein encoded by this gene is the CD3-gamma polypeptide, which together with CD3-epsilon, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T-cell receptor-CD3 complex. This complex plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. The genes encoding the epsilon, gamma and delta polypeptides are located in the same cluster on chromosome 11. Defects in this gene are associated with T cell immunodeficiency. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.11277777).
BP6
Variant 11-118349027-G-A is Benign according to our data. Variant chr11-118349027-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 541656.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.00123 (1793/1461804) while in subpopulation NFE AF= 0.00139 (1551/1111950). AF 95% confidence interval is 0.00134. There are 1 homozygotes in gnomad4_exome. There are 849 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CD3GNM_000073.3 linkuse as main transcriptc.56G>A p.Gly19Asp missense_variant, splice_region_variant 2/7 ENST00000532917.3
CD3GXM_005271724.5 linkuse as main transcriptc.56G>A p.Gly19Asp missense_variant, splice_region_variant 2/4
CD3GXM_006718941.4 linkuse as main transcriptc.56G>A p.Gly19Asp missense_variant, splice_region_variant 2/7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CD3GENST00000532917.3 linkuse as main transcriptc.56G>A p.Gly19Asp missense_variant, splice_region_variant 2/71 NM_000073.3 P1

Frequencies

GnomAD3 genomes
AF:
0.000697
AC:
106
AN:
152144
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000145
Gnomad AMI
AF:
0.00220
Gnomad AMR
AF:
0.000262
Gnomad ASJ
AF:
0.00404
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000378
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00106
Gnomad OTH
AF:
0.00192
GnomAD3 exomes
AF:
0.000744
AC:
187
AN:
251428
Hom.:
0
AF XY:
0.000765
AC XY:
104
AN XY:
135878
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.000318
Gnomad ASJ exome
AF:
0.00446
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000462
Gnomad NFE exome
AF:
0.000976
Gnomad OTH exome
AF:
0.00163
GnomAD4 exome
AF:
0.00123
AC:
1793
AN:
1461804
Hom.:
1
Cov.:
32
AF XY:
0.00117
AC XY:
849
AN XY:
727202
show subpopulations
Gnomad4 AFR exome
AF:
0.000119
Gnomad4 AMR exome
AF:
0.000358
Gnomad4 ASJ exome
AF:
0.00517
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.000449
Gnomad4 NFE exome
AF:
0.00139
Gnomad4 OTH exome
AF:
0.00104
GnomAD4 genome
AF:
0.000696
AC:
106
AN:
152262
Hom.:
1
Cov.:
32
AF XY:
0.000578
AC XY:
43
AN XY:
74440
show subpopulations
Gnomad4 AFR
AF:
0.000144
Gnomad4 AMR
AF:
0.000261
Gnomad4 ASJ
AF:
0.00404
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000378
Gnomad4 NFE
AF:
0.00106
Gnomad4 OTH
AF:
0.00190
Alfa
AF:
0.00119
Hom.:
0
Bravo
AF:
0.000722
TwinsUK
AF:
0.00108
AC:
4
ALSPAC
AF:
0.00182
AC:
7
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.00128
AC:
11
ExAC
AF:
0.000634
AC:
77
EpiCase
AF:
0.00142
EpiControl
AF:
0.000474

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:2Benign:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Combined immunodeficiency due to CD3gamma deficiency Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Likely benign, criteria provided, single submitterclinical testingInvitaeDec 26, 2023- -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2019- -
CD3G-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesNov 29, 2023This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.41
BayesDel_addAF
Benign
-0.23
T
BayesDel_noAF
Benign
-0.12
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.68
D
Eigen
Uncertain
0.44
Eigen_PC
Uncertain
0.32
FATHMM_MKL
Uncertain
0.90
D
LIST_S2
Benign
0.61
T
M_CAP
Benign
0.031
D
MetaRNN
Benign
0.11
T
MetaSVM
Benign
-0.34
T
MutationAssessor
Pathogenic
2.9
M
MutationTaster
Benign
1.0
D;N
PrimateAI
Uncertain
0.56
T
PROVEAN
Uncertain
-3.4
D
REVEL
Uncertain
0.35
Sift
Benign
0.034
D
Sift4G
Uncertain
0.043
D
Polyphen
1.0
D
Vest4
0.72
MVP
0.87
MPC
0.78
ClinPred
0.16
T
GERP RS
4.5
Varity_R
0.18
gMVP
0.67

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.76
dbscSNV1_RF
Benign
0.37
SpliceAI score (max)
0.020
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: rs146393315; hg19: chr11-118219742; API