rs1456129845
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_StrongPP5
The NM_017841.4(SDHAF2):c.355dup(p.Tyr119LeufsTer8) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,612,996 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. I118I) has been classified as Likely benign.
Frequency
Consequence
NM_017841.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDHAF2 | NM_017841.4 | c.355dup | p.Tyr119LeufsTer8 | frameshift_variant | 3/4 | ENST00000301761.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDHAF2 | ENST00000301761.7 | c.355dup | p.Tyr119LeufsTer8 | frameshift_variant | 3/4 | 1 | NM_017841.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152082Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251486Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135918
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460914Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 2AN XY: 726842
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152082Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74286
ClinVar
Submissions by phenotype
Paragangliomas 2 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jun 13, 2023 | - - |
SDHAF2-related disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 29, 2024 | The SDHAF2 c.355dupT variant is predicted to result in a frameshift and premature protein termination (p.Tyr119Leufs*8). This variant has been reported in patients with paraganglioma/pheochromocytoma tumors (Table S1 in Evenepoel L et al 2014. PubMed ID: 25394176; reported as c.357_358insT Piccini et al. 2012. PubMed ID: 22241717). This variant occurs in the 2nd to last exon and may not result in non-sense mediated decay. This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD. Frameshift variants in SDHAF2 are expected to be pathogenic. This variant is interpreted as likely pathogenic. - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2024 | The c.355dupT pathogenic mutation, located in coding exon 3 of the SDHAF2 gene, results from a duplication of T at nucleotide position 355, causing a translational frameshift with a predicted alternate stop codon (p.Y119Lfs*8). This alteration occurs at the 3' terminus of theSDHAF2 gene, is not expected to trigger nonsense-mediated mRNA decay, and only impacts the last 48 amino acids of the protein. However, premature stop codons are typically deleterious in nature and a significant portion of the protein is affected (Ambry internal data). This variant (reported as c.357_358insT in one study) has been detected in two unrelated individuals with a paraganglioma (Piccini V et al. Endocr Relat Cancer, 2012 Apr;19:149-55; Evenepoel L et al. Genet Med, 2015 Aug;17:610-20). Based on internal structural analysis, this mutation removes a large portion of the SDHAF2-SDHA interface and is likely to disrupt protein function and stability (Hao HX et al. Science, 2009 Aug;325:1139-42; Eletsky A et al. Biochemistry, 2012 Oct;51:8475-7; Sharma P et al. Proc Natl Acad Sci U S A, 2020 Sep;117:23548-23556). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 23, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: LOF not established disease mechanism for this gene - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | SDHAF2: PVS1:Strong - |
Hereditary pheochromocytoma-paraganglioma Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 20, 2023 | This sequence change creates a premature translational stop signal (p.Tyr119Leufs*8) in the SDHAF2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 48 amino acid(s) of the SDHAF2 protein. This variant is present in population databases (no rsID available, gnomAD 0.004%). This premature translational stop signal has been observed in individual(s) with a right carotid body paranglioma (PMID: 22241717). ClinVar contains an entry for this variant (Variation ID: 403423). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at