19-6665330-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001376887.1(TNFSF14):c.319G>A(p.Gly107Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000208 in 1,589,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001376887.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TNFSF14 | NM_001376887.1 | c.319G>A | p.Gly107Ser | missense_variant | 4/4 | ENST00000675206.1 | NP_001363816.1 | |
TNFSF14 | NM_003807.5 | c.319G>A | p.Gly107Ser | missense_variant | 5/5 | NP_003798.2 | ||
TNFSF14 | NM_172014.3 | c.211G>A | p.Gly71Ser | missense_variant | 4/4 | NP_742011.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TNFSF14 | ENST00000675206.1 | c.319G>A | p.Gly107Ser | missense_variant | 4/4 | NM_001376887.1 | ENSP00000502837 | P1 | ||
TNFSF14 | ENST00000599359.1 | c.319G>A | p.Gly107Ser | missense_variant | 5/5 | 1 | ENSP00000469049 | P1 | ||
TNFSF14 | ENST00000245912.7 | c.211G>A | p.Gly71Ser | missense_variant | 4/4 | 1 | ENSP00000245912 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000196 AC: 4AN: 203826Hom.: 0 AF XY: 0.0000267 AC XY: 3AN XY: 112230
GnomAD4 exome AF: 0.0000216 AC: 31AN: 1437476Hom.: 0 Cov.: 36 AF XY: 0.0000238 AC XY: 17AN XY: 713338
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152362Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.319G>A (p.G107S) alteration is located in exon 5 (coding exon 4) of the TNFSF14 gene. This alteration results from a G to A substitution at nucleotide position 319, causing the glycine (G) at amino acid position 107 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at