rs201389647
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_017841.4(SDHAF2):c.36+17T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000825 in 1,614,176 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0042 ( 1 hom., cov: 33)
Exomes 𝑓: 0.00047 ( 6 hom. )
Consequence
SDHAF2
NM_017841.4 intron
NM_017841.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.472
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 Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 11-61430199-T-C is Benign according to our data. Variant chr11-61430199-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 260943.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-61430199-T-C is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00422 (643/152352) while in subpopulation AFR AF= 0.0143 (596/41592). AF 95% confidence interval is 0.0134. There are 1 homozygotes in gnomad4. There are 314 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 643 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDHAF2 | NM_017841.4 | c.36+17T>C | intron_variant | ENST00000301761.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDHAF2 | ENST00000301761.7 | c.36+17T>C | intron_variant | 1 | NM_017841.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00423 AC: 644AN: 152234Hom.: 1 Cov.: 33
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GnomAD3 exomes AF: 0.00132 AC: 331AN: 250546Hom.: 5 AF XY: 0.000893 AC XY: 121AN XY: 135532
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GnomAD4 exome AF: 0.000471 AC: 688AN: 1461824Hom.: 6 Cov.: 31 AF XY: 0.000397 AC XY: 289AN XY: 727212
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GnomAD4 genome ? AF: 0.00422 AC: 643AN: 152352Hom.: 1 Cov.: 33 AF XY: 0.00421 AC XY: 314AN XY: 74498
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 15, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Hereditary pheochromocytoma-paraganglioma Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
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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