chr4-112278335-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000361717.4(TIFA):āc.82T>Gā(p.Cys28Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
ENST00000361717.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TIFA | NM_052864.3 | c.82T>G | p.Cys28Gly | missense_variant | 2/2 | ENST00000361717.4 | NP_443096.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TIFA | ENST00000361717.4 | c.82T>G | p.Cys28Gly | missense_variant | 2/2 | 1 | NM_052864.3 | ENSP00000354911.2 | ||
TIFA | ENST00000500655.2 | c.82T>G | p.Cys28Gly | missense_variant | 2/2 | 3 | ENSP00000424231.1 | |||
TIFA | ENST00000610220.2 | c.82T>G | p.Cys28Gly | missense_variant | 2/2 | 6 | ENSP00000516322.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000561 AC: 14AN: 249696Hom.: 0 AF XY: 0.0000814 AC XY: 11AN XY: 135114
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461022Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 726772
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152288Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.82T>G (p.C28G) alteration is located in exon 2 (coding exon 1) of the TIFA gene. This alteration results from a T to G substitution at nucleotide position 82, causing the cysteine (C) at amino acid position 28 to be replaced by a glycine (G). 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