8-23154967-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003840.5(TNFRSF10D):c.163T>C(p.Ser55Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,612,080 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003840.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF10D | NM_003840.5 | c.163T>C | p.Ser55Pro | missense_variant | 2/9 | ENST00000312584.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF10D | ENST00000312584.4 | c.163T>C | p.Ser55Pro | missense_variant | 2/9 | 1 | NM_003840.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000164 AC: 25AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000283 AC: 7AN: 247398Hom.: 0 AF XY: 0.0000374 AC XY: 5AN XY: 133628
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1459822Hom.: 1 Cov.: 31 AF XY: 0.00000964 AC XY: 7AN XY: 726022
GnomAD4 genome ? AF: 0.000164 AC: 25AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.163T>C (p.S55P) alteration is located in exon 2 (coding exon 2) of the TNFRSF10D gene. This alteration results from a T to C substitution at nucleotide position 163, causing the serine (S) at amino acid position 55 to be replaced by a proline (P). 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