rs858543

Variant summary

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

The NM_198053.3(CD247):​c.58+20347T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.738 in 152,074 control chromosomes in the GnomAD database, including 41,586 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 0.74 ( 41586 hom., cov: 31)

Consequence

CD247
NM_198053.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.571
Variant links:
Genes affected
CD247 (HGNC:1677): (CD247 molecule) The protein encoded by this gene is T-cell receptor zeta, which together with T-cell receptor alpha/beta and gamma/delta heterodimers, and with CD3-gamma, -delta and -epsilon, forms the T-cell receptor-CD3 complex. The zeta chain plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. Low expression of the antigen results in impaired immune response. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CD247NM_198053.3 linkuse as main transcriptc.58+20347T>C intron_variant ENST00000362089.10 NP_932170.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD247ENST00000362089.10 linkuse as main transcriptc.58+20347T>C intron_variant 1 NM_198053.3 ENSP00000354782 A1P20963-1

Frequencies

GnomAD3 genomes
AF:
0.738
AC:
112095
AN:
151954
Hom.:
41543
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.764
Gnomad AMI
AF:
0.533
Gnomad AMR
AF:
0.752
Gnomad ASJ
AF:
0.700
Gnomad EAS
AF:
0.495
Gnomad SAS
AF:
0.739
Gnomad FIN
AF:
0.746
Gnomad MID
AF:
0.646
Gnomad NFE
AF:
0.741
Gnomad OTH
AF:
0.725
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.738
AC:
112188
AN:
152074
Hom.:
41586
Cov.:
31
AF XY:
0.736
AC XY:
54694
AN XY:
74324
show subpopulations
Gnomad4 AFR
AF:
0.764
Gnomad4 AMR
AF:
0.752
Gnomad4 ASJ
AF:
0.700
Gnomad4 EAS
AF:
0.495
Gnomad4 SAS
AF:
0.739
Gnomad4 FIN
AF:
0.746
Gnomad4 NFE
AF:
0.741
Gnomad4 OTH
AF:
0.718
Alfa
AF:
0.733
Hom.:
49931
Bravo
AF:
0.734
Asia WGS
AF:
0.619
AC:
2155
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
1.3
DANN
Benign
0.70

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs858543; hg19: chr1-167467298; API