rs62624461
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_020186.3(SDHAF3):c.157T>C(p.Phe53Leu) variant causes a missense change. The variant allele was found at a frequency of 0.024 in 1,614,092 control chromosomes in the GnomAD database, including 520 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 0.018 ( 35 hom., cov: 33)
Exomes 𝑓: 0.025 ( 485 hom. )
Consequence
SDHAF3
NM_020186.3 missense
NM_020186.3 missense
Scores
3
8
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.69
Genes affected
SDHAF3 (HGNC:21752): (succinate dehydrogenase complex assembly factor 3) Predicted to be involved in mitochondrial respiratory chain complex II assembly; regulation of gluconeogenesis; and succinate metabolic process. Predicted to be located in mitochondrial matrix. Predicted to be active in mitochondrial intermembrane space. [provided by Alliance of Genome Resources, Apr 2022]
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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 (MetaRNN=0.008035541).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0177 (2693/152324) while in subpopulation NFE AF= 0.0262 (1781/68020). AF 95% confidence interval is 0.0252. There are 35 homozygotes in gnomad4. There are 1306 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 35 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDHAF3 | NM_020186.3 | c.157T>C | p.Phe53Leu | missense_variant | 1/2 | ENST00000432641.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDHAF3 | ENST00000432641.3 | c.157T>C | p.Phe53Leu | missense_variant | 1/2 | 1 | NM_020186.3 | P1 | |
SDHAF3 | ENST00000360382.4 | c.157T>C | p.Phe53Leu | missense_variant | 1/3 | 2 | |||
SDHAF3 | ENST00000489852.1 | n.180T>C | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0177 AC: 2696AN: 152206Hom.: 35 Cov.: 33
GnomAD3 genomes
?
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2696
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33
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GnomAD3 exomes AF: 0.0202 AC: 5026AN: 248826Hom.: 70 AF XY: 0.0217 AC XY: 2926AN XY: 134680
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GnomAD4 exome AF: 0.0246 AC: 36028AN: 1461768Hom.: 485 Cov.: 30 AF XY: 0.0251 AC XY: 18232AN XY: 727168
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GnomAD4 genome ? AF: 0.0177 AC: 2693AN: 152324Hom.: 35 Cov.: 33 AF XY: 0.0175 AC XY: 1306AN XY: 74490
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ALSPAC
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108
ESP6500AA
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28
ESP6500EA
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214
ExAC
?
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2529
Asia WGS
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41
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3478
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Uncertain
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Pathogenic
D;D
Sift4G
Benign
T;T
Polyphen
P;.
Vest4
MutPred
Gain of loop (P = 0.1069);Gain of loop (P = 0.1069);
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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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