3-172506513-A-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003810.4(TNFSF10):c.825T>A(p.Phe275Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. F275F) has been classified as Benign.
Frequency
Consequence
NM_003810.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFSF10 | NM_003810.4 | c.825T>A | p.Phe275Leu | missense_variant | 5/5 | ENST00000241261.7 | |
TNFSF10 | NM_001190942.2 | c.*371T>A | 3_prime_UTR_variant | 3/3 | |||
TNFSF10 | NR_033994.2 | n.828T>A | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFSF10 | ENST00000241261.7 | c.825T>A | p.Phe275Leu | missense_variant | 5/5 | 1 | NM_003810.4 | P1 | |
TNFSF10 | ENST00000420541.6 | c.*371T>A | 3_prime_UTR_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 152018Hom.: 0 Cov.: 32 FAILED QC
GnomAD4 exome Cov.: 61
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74262
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at