16-57977824-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000441824.4(TEPP):c.8G>A(p.Arg3His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,612,838 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3C) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000441824.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPMIP8 | NM_199456.3 | c.8G>A | p.Arg3His | missense_variant | 2/8 | ENST00000441824.4 | NP_955535.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TEPP | ENST00000441824.4 | c.8G>A | p.Arg3His | missense_variant | 2/8 | 1 | NM_199456.3 | ENSP00000401917.3 | ||
TEPP | ENST00000290871.10 | c.8G>A | p.Arg3His | missense_variant | 2/8 | 1 | ENSP00000290871.6 | |||
TEPP | ENST00000569996.5 | n.57+1190G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152202Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000998 AC: 25AN: 250468Hom.: 0 AF XY: 0.0000960 AC XY: 13AN XY: 135396
GnomAD4 exome AF: 0.0000630 AC: 92AN: 1460518Hom.: 0 Cov.: 31 AF XY: 0.0000730 AC XY: 53AN XY: 726354
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152320Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | The c.173G>A (p.R58H) alteration is located in exon 2 (coding exon 2) of the TEPP gene. This alteration results from a G to A substitution at nucleotide position 173, causing the arginine (R) at amino acid position 58 to be replaced by a histidine (H). 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