16-20360584-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_174924.2(PDILT):c.1490T>C(p.Ile497Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,546 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 (★).
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.1490T>C | p.Ile497Thr | missense_variant | 11/12 | ENST00000302451.9 | |
PDILT | XM_011545766.4 | c.668T>C | p.Ile223Thr | missense_variant | 7/8 | ||
PDILT | XM_011545765.2 | c.*113T>C | 3_prime_UTR_variant | 10/10 | |||
PDILT | XR_950754.2 | n.1560T>C | non_coding_transcript_exon_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDILT | ENST00000302451.9 | c.1490T>C | p.Ile497Thr | missense_variant | 11/12 | 1 | NM_174924.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251428Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461476Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 727078
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.1490T>C (p.I497T) alteration is located in exon 11 (coding exon 10) of the PDILT gene. This alteration results from a T to C substitution at nucleotide position 1490, causing the isoleucine (I) at amino acid position 497 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