rs4149584
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_001065.4(TNFRSF1A):c.362G>C(p.Arg121Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R121Q) has been classified as Likely benign.
Frequency
Consequence
NM_001065.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNFRSF1A | NM_001065.4 | c.362G>C | p.Arg121Pro | missense_variant | 4/10 | ENST00000162749.7 | |
TNFRSF1A | NM_001346091.2 | c.38G>C | p.Arg13Pro | missense_variant | 3/9 | ||
TNFRSF1A | NM_001346092.2 | c.-216G>C | 5_prime_UTR_variant | 4/11 | |||
TNFRSF1A | NR_144351.2 | n.624G>C | non_coding_transcript_exon_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNFRSF1A | ENST00000162749.7 | c.362G>C | p.Arg121Pro | missense_variant | 4/10 | 1 | NM_001065.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151494Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251342Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135826
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461874Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727236
GnomAD4 genome ? Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 151494Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73948
ClinVar
Submissions by phenotype
TNF receptor-associated periodic fever syndrome (TRAPS) Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2001 | - - |
not provided, no classification provided | literature only | Unité médicale des maladies autoinflammatoires, CHRU Montpellier | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at