rs535627239
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_017841.4(SDHAF2):c.320G>A(p.Arg107His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,614,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_017841.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SDHAF2 | ENST00000301761.7 | c.320G>A | p.Arg107His | missense_variant | Exon 3 of 4 | 1 | NM_017841.4 | ENSP00000301761.3 | ||
ENSG00000256591 | ENST00000541135.5 | c.320G>A | p.Arg107His | missense_variant | Exon 3 of 5 | 4 | ENSP00000443130.1 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000199 AC: 50AN: 251478Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135916
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461870Hom.: 0 Cov.: 33 AF XY: 0.0000619 AC XY: 45AN XY: 727244
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74362
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Benign:2
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
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Ovarian cancer Pathogenic:1
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Paragangliomas 2 Uncertain:1
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Hereditary pheochromocytoma-paraganglioma Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at