chr16-67155227-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_003789.4(TRADD):c.497C>T(p.Ser166Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000356 in 1,602,562 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_003789.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRADD | NM_003789.4 | c.497C>T | p.Ser166Leu | missense_variant | 4/5 | ENST00000345057.9 | |
TRADD | NM_001323552.2 | c.497C>T | p.Ser166Leu | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRADD | ENST00000345057.9 | c.497C>T | p.Ser166Leu | missense_variant | 4/5 | 1 | NM_003789.4 | P1 | |
TRADD | ENST00000486556.1 | c.317C>T | p.Ser106Leu | missense_variant | 2/3 | 2 | |||
TRADD | ENST00000566247.1 | n.192C>T | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000889 AC: 2AN: 224978Hom.: 0 AF XY: 0.00000808 AC XY: 1AN XY: 123754
GnomAD4 exome AF: 0.0000317 AC: 46AN: 1450318Hom.: 0 Cov.: 36 AF XY: 0.0000305 AC XY: 22AN XY: 720792
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74392
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 16, 2023 | The c.497C>T (p.S166L) alteration is located in exon 4 (coding exon 3) of the TRADD gene. This alteration results from a C to T substitution at nucleotide position 497, causing the serine (S) at amino acid position 166 to be replaced by a leucine (L). 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