rs752462796
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_017841.4(SDHAF2):c.194C>A(p.Thr65Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Consequence
SDHAF2
NM_017841.4 missense
NM_017841.4 missense
Scores
7
12
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.38
Genes affected
SDHAF2 (HGNC:26034): (succinate dehydrogenase complex assembly factor 2) This gene encodes a mitochondrial assembly factor needed for the flavination of a succinate dehydrogenase complex subunit (SDHA), which is required for activity of the succinate dehydrogenase complex. Mutations in this gene are associated with paraganglioma. [provided by RefSeq, May 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.31616104).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHAF2 | NM_017841.4 | c.194C>A | p.Thr65Asn | missense_variant | 2/4 | ENST00000301761.7 | NP_060311.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDHAF2 | ENST00000301761.7 | c.194C>A | p.Thr65Asn | missense_variant | 2/4 | 1 | NM_017841.4 | ENSP00000301761.3 | ||
ENSG00000256591 | ENST00000541135.5 | c.194C>A | p.Thr65Asn | missense_variant | 2/5 | 4 | ENSP00000443130.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;T;D;D;D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
.;M;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.;.;D
REVEL
Uncertain
Sift
Benign
D;D;.;.;D
Sift4G
Uncertain
T;T;D;D;D
Polyphen
0.83
.;P;.;.;.
Vest4
0.29, 0.28, 0.30, 0.30
MutPred
Loss of phosphorylation at T65 (P = 0.0337);Loss of phosphorylation at T65 (P = 0.0337);Loss of phosphorylation at T65 (P = 0.0337);Loss of phosphorylation at T65 (P = 0.0337);Loss of phosphorylation at T65 (P = 0.0337);
MVP
MPC
0.20
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.