rs168259

Variant summary

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

The ENST00000597430.2(CD70):​c.-213-3193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,178 control chromosomes in the GnomAD database, including 1,309 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 0.13 ( 1309 hom., cov: 32)

Consequence

CD70
ENST00000597430.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.221
Variant links:
Genes affected
CD70 (HGNC:11937): (CD70 molecule) The protein encoded by this gene is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This cytokine is a ligand for TNFRSF27/CD27. It is a surface antigen on activated, but not on resting, T and B lymphocytes. It induces proliferation of costimulated T cells, enhances the generation of cytolytic T cells, and contributes to T cell activation. This cytokine is also reported to play a role in regulating B-cell activation, cytotoxic function of natural killer cells, and immunoglobulin sythesis. [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=-0.94).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD70ENST00000597430.2 linkc.-213-3193C>T intron_variant Intron 1 of 3 3 ENSP00000470805.2 M0QZW2

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
19103
AN:
152060
Hom.:
1304
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.146
Gnomad AMI
AF:
0.222
Gnomad AMR
AF:
0.110
Gnomad ASJ
AF:
0.121
Gnomad EAS
AF:
0.0899
Gnomad SAS
AF:
0.167
Gnomad FIN
AF:
0.0368
Gnomad MID
AF:
0.149
Gnomad NFE
AF:
0.129
Gnomad OTH
AF:
0.122
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.126
AC:
19133
AN:
152178
Hom.:
1309
Cov.:
32
AF XY:
0.122
AC XY:
9073
AN XY:
74412
show subpopulations
Gnomad4 AFR
AF:
0.146
Gnomad4 AMR
AF:
0.110
Gnomad4 ASJ
AF:
0.121
Gnomad4 EAS
AF:
0.0905
Gnomad4 SAS
AF:
0.168
Gnomad4 FIN
AF:
0.0368
Gnomad4 NFE
AF:
0.129
Gnomad4 OTH
AF:
0.124
Alfa
AF:
0.130
Hom.:
1725
Bravo
AF:
0.130
Asia WGS
AF:
0.128
AC:
444
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
3.2
DANN
Benign
0.74

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: rs168259; hg19: chr19-6595779; API