8-23191906-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003844.4(TNFRSF10A):c.1195G>A(p.Ala399Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A399G) has been classified as Uncertain significance.
Frequency
Consequence
NM_003844.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF10A | ENST00000221132.8 | c.1195G>A | p.Ala399Thr | missense_variant | Exon 10 of 10 | 1 | NM_003844.4 | ENSP00000221132.3 | ||
TNFRSF10A | ENST00000613472.1 | c.721G>A | p.Ala241Thr | missense_variant | Exon 9 of 9 | 1 | ENSP00000480778.1 | |||
TNFRSF10A | ENST00000519862.1 | n.250G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251472Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135912
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461894Hom.: 0 Cov.: 35 AF XY: 0.00000275 AC XY: 2AN XY: 727248
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1195G>A (p.A399T) alteration is located in exon 10 (coding exon 10) of the TNFRSF10A gene. This alteration results from a G to A substitution at nucleotide position 1195, causing the alanine (A) at amino acid position 399 to be replaced by a threonine (T). 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