rs13398676
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_015650.4(TRAF3IP1):c.69C>A(p.Thr23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 1,446,688 control chromosomes in the GnomAD database, including 372,651 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. T23T) has been classified as Likely benign.
Frequency
Consequence
NM_015650.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.69C>A | p.Thr23= | synonymous_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.69C>A | p.Thr23= | synonymous_variant | 1/17 | 1 | NM_015650.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.69C>A | p.Thr23= | synonymous_variant | 1/15 | 1 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.69C>A | p.Thr23= | synonymous_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.723 AC: 109206AN: 151060Hom.: 39660 Cov.: 33
GnomAD3 exomes AF: 0.725 AC: 72412AN: 99838Hom.: 26737 AF XY: 0.724 AC XY: 39707AN XY: 54856
GnomAD4 exome AF: 0.715 AC: 925850AN: 1295520Hom.: 332952 Cov.: 56 AF XY: 0.716 AC XY: 457730AN XY: 639182
GnomAD4 genome ? AF: 0.723 AC: 109295AN: 151168Hom.: 39699 Cov.: 33 AF XY: 0.724 AC XY: 53489AN XY: 73862
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Senior-Loken syndrome 9 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at