chr14-19416319-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001005356.3(POTEG):āc.1166G>Cā(p.Arg389Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000873 in 145,508 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001005356.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POTEG | NM_001005356.3 | c.1166G>C | p.Arg389Thr | missense_variant | 7/11 | ENST00000547848.5 | |
POTEG | NR_027480.2 | n.1218G>C | non_coding_transcript_exon_variant | 7/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POTEG | ENST00000547848.5 | c.1166G>C | p.Arg389Thr | missense_variant | 7/11 | 1 | NM_001005356.3 | P1 | |
POTEG | ENST00000622767.4 | c.1166G>C | p.Arg389Thr | missense_variant, NMD_transcript_variant | 7/12 | 1 | |||
POTEG | ENST00000547722.1 | c.*453G>C | 3_prime_UTR_variant, NMD_transcript_variant | 8/12 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000873 AC: 127AN: 145500Hom.: 0 Cov.: 30
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000545 AC: 762AN: 1399408Hom.: 0 Cov.: 35 AF XY: 0.000558 AC XY: 388AN XY: 695714
GnomAD4 genome AF: 0.000873 AC: 127AN: 145508Hom.: 0 Cov.: 30 AF XY: 0.000920 AC XY: 65AN XY: 70656
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.1166G>C (p.R389T) alteration is located in exon 7 (coding exon 7) of the POTEG gene. This alteration results from a G to C substitution at nucleotide position 1166, causing the arginine (R) at amino acid position 389 to be replaced by a threonine (T). 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