rs104895252
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The ENST00000162749.7(TNFRSF1A):c.215G>T(p.Cys72Phe) 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. Variant has been reported in ClinVar as Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C72S) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000162749.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF1A | NM_001065.4 | c.215G>T | p.Cys72Phe | missense_variant | 3/10 | ENST00000162749.7 | NP_001056.1 | |
TNFRSF1A | NM_001346091.2 | c.-110G>T | 5_prime_UTR_variant | 2/9 | NP_001333020.1 | |||
TNFRSF1A | NM_001346092.2 | c.-363G>T | 5_prime_UTR_variant | 3/11 | NP_001333021.1 | |||
TNFRSF1A | NR_144351.2 | n.477G>T | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF1A | ENST00000162749.7 | c.215G>T | p.Cys72Phe | missense_variant | 3/10 | 1 | NM_001065.4 | ENSP00000162749 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1448878Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 719662
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Autoinflammatory syndrome Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Apr 16, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.