chr2-238320730-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015650.4(TRAF3IP1):c.68C>T(p.Thr23Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000551 in 1,452,894 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Synonymous variant affecting the same amino acid position (i.e. T23T) has been classified as Benign.
Frequency
Consequence
NM_015650.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TRAF3IP1 | NM_015650.4 | c.68C>T | p.Thr23Ile | missense_variant | 1/17 | ENST00000373327.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRAF3IP1 | ENST00000373327.5 | c.68C>T | p.Thr23Ile | missense_variant | 1/17 | 1 | NM_015650.4 | ||
TRAF3IP1 | ENST00000391993.7 | c.68C>T | p.Thr23Ile | missense_variant | 1/15 | 1 | P1 | ||
TRAF3IP1 | ENST00000409739.2 | c.68C>T | p.Thr23Ile | missense_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000494 AC: 5AN: 101182Hom.: 0 AF XY: 0.0000360 AC XY: 2AN XY: 55512
GnomAD4 exome AF: 0.00000538 AC: 7AN: 1301646Hom.: 0 Cov.: 30 AF XY: 0.00000467 AC XY: 3AN XY: 642274
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151248Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 73844
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2021 | The c.68C>T (p.T23I) alteration is located in exon 1 (coding exon 1) of the TRAF3IP1 gene. This alteration results from a C to T substitution at nucleotide position 68, causing the threonine (T) at amino acid position 23 to be replaced by an isoleucine (I). 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