chr19-6586058-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001252.5(CD70):​c.544G>A​(p.Asp182Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as other (no stars).

Frequency

Genomes: not found (cov: 31)

Consequence

CD70
NM_001252.5 missense

Scores

3
6
10

Clinical Significance

- - O:1

Conservation

PhyloP100: 1.92
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD70NM_001252.5 linkc.544G>A p.Asp182Asn missense_variant Exon 3 of 3 ENST00000245903.4 NP_001243.1 P32970-1A0A0U5JA32
CD70NM_001330332.2 linkc.448+96G>A intron_variant Intron 3 of 3 NP_001317261.1 P32970-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD70ENST00000245903.4 linkc.544G>A p.Asp182Asn missense_variant Exon 3 of 3 1 NM_001252.5 ENSP00000245903.2 P32970-1
CD70ENST00000423145.7 linkc.448+96G>A intron_variant Intron 3 of 3 2 ENSP00000395294.2 P32970-2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
31

ClinVar

Significance: -
Submissions summary: Other:1
Revision: -
LINK: link

Submissions by phenotype

Neoplasm Other:1
Mar 04, 2025
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital
Significance: -
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.62
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.43
CADD
Benign
23
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.89
D
Eigen
Benign
0.13
Eigen_PC
Benign
0.0038
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.81
T
M_CAP
Uncertain
0.14
D
MetaRNN
Uncertain
0.68
D
MetaSVM
Benign
-0.47
T
MutationAssessor
Benign
1.7
L
PrimateAI
Uncertain
0.52
T
PROVEAN
Uncertain
-4.2
D
REVEL
Benign
0.25
Sift
Uncertain
0.0080
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.37
MutPred
0.48
Gain of catalytic residue at T181 (P = 0.0874);
MVP
0.79
MPC
1.4
ClinPred
0.99
D
GERP RS
4.3
Varity_R
0.39

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-6586069; COSMIC: COSV55565444; COSMIC: COSV55565444; API