16-20369517-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_174924.2(PDILT):c.1091G>A(p.Arg364His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00044 in 1,614,104 control chromosomes in the GnomAD database, including 3 homozygotes. 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. R364C) has been classified as Uncertain significance.
Frequency
Consequence
NM_174924.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDILT | NM_174924.2 | c.1091G>A | p.Arg364His | missense_variant | 8/12 | ENST00000302451.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDILT | ENST00000302451.9 | c.1091G>A | p.Arg364His | missense_variant | 8/12 | 1 | NM_174924.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000361 AC: 55AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000342 AC: 86AN: 251452Hom.: 2 AF XY: 0.000309 AC XY: 42AN XY: 135904
GnomAD4 exome AF: 0.000449 AC: 656AN: 1461790Hom.: 3 Cov.: 31 AF XY: 0.000444 AC XY: 323AN XY: 727188
GnomAD4 genome ? AF: 0.000361 AC: 55AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 06, 2022 | The c.1091G>A (p.R364H) alteration is located in exon 8 (coding exon 7) of the PDILT gene. This alteration results from a G to A substitution at nucleotide position 1091, causing the arginine (R) at amino acid position 364 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