16-20362415-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_174924.2(PDILT):c.1405G>A(p.Gly469Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000613 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_174924.2 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 |
---|---|---|---|---|---|---|---|
PDILT | NM_174924.2 | c.1405G>A | p.Gly469Ser | missense_variant | 10/12 | ENST00000302451.9 | |
PDILT | XM_011545766.4 | c.583G>A | p.Gly195Ser | missense_variant | 6/8 | ||
PDILT | XM_011545765.2 | c.*40-1758G>A | intron_variant | ||||
PDILT | XR_950754.2 | n.1487-1758G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDILT | ENST00000302451.9 | c.1405G>A | p.Gly469Ser | missense_variant | 10/12 | 1 | NM_174924.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251094Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135690
GnomAD4 exome AF: 0.0000609 AC: 89AN: 1461750Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727166
GnomAD4 genome ? AF: 0.0000657 AC: 10AN: 152294Hom.: 0 Cov.: 31 AF XY: 0.0000671 AC XY: 5AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2021 | The c.1405G>A (p.G469S) alteration is located in exon 10 (coding exon 9) of the PDILT gene. This alteration results from a G to A substitution at nucleotide position 1405, causing the glycine (G) at amino acid position 469 to be replaced by a serine (S). 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