rs870875

Variant summary

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

The ENST00000700105.1(CD247):​c.429+2527T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.377 in 394,626 control chromosomes in the GnomAD database, including 28,781 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 0.37 ( 10630 hom., cov: 33)
Exomes 𝑓: 0.38 ( 18151 hom. )

Consequence

CD247
ENST00000700105.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.787
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]

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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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
use as main transcriptn.167430497A>C intergenic_region

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD247ENST00000700105.1 linkuse as main transcriptc.429+2527T>G intron_variant ENSP00000514800.1 A0A8V8TQY8

Frequencies

GnomAD3 genomes
AF:
0.368
AC:
55995
AN:
152102
Hom.:
10608
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.301
Gnomad AMI
AF:
0.455
Gnomad AMR
AF:
0.469
Gnomad ASJ
AF:
0.304
Gnomad EAS
AF:
0.430
Gnomad SAS
AF:
0.455
Gnomad FIN
AF:
0.484
Gnomad MID
AF:
0.259
Gnomad NFE
AF:
0.361
Gnomad OTH
AF:
0.350
GnomAD4 exome
AF:
0.382
AC:
92698
AN:
242406
Hom.:
18151
AF XY:
0.382
AC XY:
46916
AN XY:
122876
show subpopulations
Gnomad4 AFR exome
AF:
0.302
Gnomad4 AMR exome
AF:
0.523
Gnomad4 ASJ exome
AF:
0.321
Gnomad4 EAS exome
AF:
0.455
Gnomad4 SAS exome
AF:
0.481
Gnomad4 FIN exome
AF:
0.472
Gnomad4 NFE exome
AF:
0.361
Gnomad4 OTH exome
AF:
0.375
GnomAD4 genome
AF:
0.368
AC:
56060
AN:
152220
Hom.:
10630
Cov.:
33
AF XY:
0.379
AC XY:
28216
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.301
Gnomad4 AMR
AF:
0.470
Gnomad4 ASJ
AF:
0.304
Gnomad4 EAS
AF:
0.429
Gnomad4 SAS
AF:
0.455
Gnomad4 FIN
AF:
0.484
Gnomad4 NFE
AF:
0.361
Gnomad4 OTH
AF:
0.351
Alfa
AF:
0.365
Hom.:
16366
Bravo
AF:
0.368
Asia WGS
AF:
0.412
AC:
1433
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.47
DANN
Benign
0.67

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: rs870875; hg19: chr1-167399734; API