rs4149637
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_001346091.2(TNFRSF1A):c.-101C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00467 in 1,599,400 control chromosomes in the GnomAD database, including 272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001346091.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0230 AC: 3500AN: 152142Hom.: 138 Cov.: 32
GnomAD3 exomes AF: 0.00574 AC: 1290AN: 224860Hom.: 47 AF XY: 0.00421 AC XY: 510AN XY: 121194
GnomAD4 exome AF: 0.00274 AC: 3962AN: 1447140Hom.: 133 Cov.: 33 AF XY: 0.00241 AC XY: 1735AN XY: 718564
GnomAD4 genome AF: 0.0231 AC: 3513AN: 152260Hom.: 139 Cov.: 32 AF XY: 0.0214 AC XY: 1596AN XY: 74432
ClinVar
Submissions by phenotype
not provided Benign:3
This variant is associated with the following publications: (PMID: 16569687, 24393624, 11443543, 27872575, 21420073, 20981092, 23894535, 24233262, 27884173) -
- -
- -
TNF receptor-associated periodic fever syndrome (TRAPS) Benign:3
- -
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
- -
Autoinflammatory syndrome Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at