1-246759053-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_016002.3(SCCPDH):c.715C>T(p.Arg239Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000181 in 1,604,664 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016002.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SCCPDH | NM_016002.3 | c.715C>T | p.Arg239Trp | missense_variant | Exon 7 of 12 | ENST00000366510.4 | NP_057086.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251326Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135824
GnomAD4 exome AF: 0.000186 AC: 270AN: 1452560Hom.: 1 Cov.: 27 AF XY: 0.000169 AC XY: 122AN XY: 723348
GnomAD4 genome AF: 0.000138 AC: 21AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.715C>T (p.R239W) alteration is located in exon 7 (coding exon 7) of the SCCPDH gene. This alteration results from a C to T substitution at nucleotide position 715, causing the arginine (R) at amino acid position 239 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