16-67155495-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003789.4(TRADD):c.311C>T(p.Ala104Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000739 in 1,555,790 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRADD | NM_003789.4 | c.311C>T | p.Ala104Val | missense_variant | 3/5 | ENST00000345057.9 | |
TRADD | NM_001323552.2 | c.311C>T | p.Ala104Val | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRADD | ENST00000345057.9 | c.311C>T | p.Ala104Val | missense_variant | 3/5 | 1 | NM_003789.4 | P1 | |
TRADD | ENST00000486556.1 | c.131C>T | p.Ala44Val | missense_variant | 1/3 | 2 | |||
TRADD | ENST00000563348.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000779 AC: 12AN: 154090Hom.: 1 AF XY: 0.0000588 AC XY: 5AN XY: 85090
GnomAD4 exome AF: 0.0000755 AC: 106AN: 1403562Hom.: 1 Cov.: 35 AF XY: 0.0000648 AC XY: 45AN XY: 694516
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2022 | The c.311C>T (p.A104V) alteration is located in exon 3 (coding exon 2) of the TRADD gene. This alteration results from a C to T substitution at nucleotide position 311, causing the alanine (A) at amino acid position 104 to be replaced by a valine (V). 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