chr6-170584376-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002598.4(PDCD2):c.206C>G(p.Pro69Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00355 in 1,490,742 control chromosomes in the GnomAD database, including 175 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.019 ( 97 hom., cov: 33)
Exomes 𝑓: 0.0018 ( 78 hom. )
Consequence
PDCD2
NM_002598.4 missense
NM_002598.4 missense
Scores
1
2
15
Clinical Significance
Conservation
PhyloP100: 1.28
Genes affected
PDCD2 (HGNC:8762): (programmed cell death 2) This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0031739473).
BP6
?
Variant 6-170584376-G-C is Benign according to our data. Variant chr6-170584376-G-C is described in ClinVar as [Benign]. Clinvar id is 784105.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0639 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDCD2 | NM_002598.4 | c.206C>G | p.Pro69Arg | missense_variant | 1/6 | ENST00000541970.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDCD2 | ENST00000541970.6 | c.206C>G | p.Pro69Arg | missense_variant | 1/6 | 1 | NM_002598.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0189 AC: 2879AN: 152168Hom.: 98 Cov.: 33
GnomAD3 genomes
?
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2879
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GnomAD3 exomes AF: 0.00414 AC: 602AN: 145504Hom.: 12 AF XY: 0.00317 AC XY: 265AN XY: 83696
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GnomAD4 exome AF: 0.00181 AC: 2419AN: 1338456Hom.: 78 Cov.: 32 AF XY: 0.00168 AC XY: 1114AN XY: 664752
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GnomAD4 genome ? AF: 0.0189 AC: 2876AN: 152286Hom.: 97 Cov.: 33 AF XY: 0.0174 AC XY: 1295AN XY: 74464
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ExAC
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Asia WGS
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3476
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 02, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;.;.;.;.;T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;.;M;.;.;.
MutationTaster
Benign
N;N;N;N;N;N
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;N;.;N
REVEL
Benign
Sift
Benign
T;T;T;T;T;.;T
Sift4G
Benign
T;T;T;T;T;T;T
Polyphen
B;.;P;.;.;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at