rs2234163
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_003820.4(TNFRSF14):c.349G>A(p.Ala117Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00885 in 1,606,292 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003820.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFRSF14 | NM_003820.4 | c.349G>A | p.Ala117Thr | missense_variant | 4/8 | ENST00000355716.5 | NP_003811.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFRSF14 | ENST00000355716.5 | c.349G>A | p.Ala117Thr | missense_variant | 4/8 | 1 | NM_003820.4 | ENSP00000347948 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0152 AC: 2321AN: 152232Hom.: 34 Cov.: 33
GnomAD3 exomes AF: 0.0107 AC: 2503AN: 233130Hom.: 32 AF XY: 0.0102 AC XY: 1288AN XY: 126526
GnomAD4 exome AF: 0.00817 AC: 11881AN: 1453942Hom.: 106 Cov.: 34 AF XY: 0.00819 AC XY: 5918AN XY: 722526
GnomAD4 genome AF: 0.0153 AC: 2332AN: 152350Hom.: 36 Cov.: 33 AF XY: 0.0146 AC XY: 1091AN XY: 74488
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at