7-97117733-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020186.3(SDHAF3):c.10C>T(p.Arg4Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000176 in 1,612,600 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020186.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDHAF3 | NM_020186.3 | c.10C>T | p.Arg4Trp | missense_variant | 1/2 | ENST00000432641.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDHAF3 | ENST00000432641.3 | c.10C>T | p.Arg4Trp | missense_variant | 1/2 | 1 | NM_020186.3 | P1 | |
SDHAF3 | ENST00000360382.4 | c.10C>T | p.Arg4Trp | missense_variant | 1/3 | 2 | |||
SDHAF3 | ENST00000489852.1 | n.33C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000129 AC: 32AN: 248336Hom.: 0 AF XY: 0.000119 AC XY: 16AN XY: 134318
GnomAD4 exome AF: 0.000181 AC: 265AN: 1460380Hom.: 0 Cov.: 30 AF XY: 0.000164 AC XY: 119AN XY: 726418
GnomAD4 genome AF: 0.000125 AC: 19AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000941 AC XY: 7AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | The c.10C>T (p.R4W) alteration is located in exon 1 (coding exon 1) of the SDHAF3 gene. This alteration results from a C to T substitution at nucleotide position 10, causing the arginine (R) at amino acid position 4 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at