rs13475
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020186.3(SDHAF3):c.*202G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 426,262 control chromosomes in the GnomAD database, including 77,639 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 0.59 ( 26533 hom., cov: 32)
Exomes 𝑓: 0.61 ( 51106 hom. )
Consequence
SDHAF3
NM_020186.3 3_prime_UTR
NM_020186.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.145
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 (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDHAF3 | NM_020186.3 | c.*202G>A | 3_prime_UTR_variant | 2/2 | ENST00000432641.3 | ||
LOC124901704 | XR_007060445.1 | n.132-1068C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDHAF3 | ENST00000432641.3 | c.*202G>A | 3_prime_UTR_variant | 2/2 | 1 | NM_020186.3 | P1 | ||
SDHAF3 | ENST00000360382.4 | c.*453G>A | 3_prime_UTR_variant | 3/3 | 2 | ||||
SDHAF3 | ENST00000479853.1 | n.544G>A | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.589 AC: 89414AN: 151846Hom.: 26519 Cov.: 32
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GnomAD4 exome AF: 0.608 AC: 166708AN: 274298Hom.: 51106 Cov.: 4 AF XY: 0.606 AC XY: 86287AN XY: 142312
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GnomAD4 genome ? AF: 0.589 AC: 89471AN: 151964Hom.: 26533 Cov.: 32 AF XY: 0.587 AC XY: 43590AN XY: 74268
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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