10-95238092-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020992.4(PDLIM1):c.823C>T(p.Arg275Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,608 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R275Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_020992.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDLIM1 | NM_020992.4 | c.823C>T | p.Arg275Trp | missense_variant | 7/7 | ENST00000329399.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDLIM1 | ENST00000329399.7 | c.823C>T | p.Arg275Trp | missense_variant | 7/7 | 1 | NM_020992.4 | P1 | |
PDLIM1 | ENST00000477757.5 | n.768C>T | non_coding_transcript_exon_variant | 6/6 | 2 | ||||
PDLIM1 | ENST00000492511.1 | n.301C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249250Hom.: 0 AF XY: 0.0000816 AC XY: 11AN XY: 134812
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461468Hom.: 0 Cov.: 32 AF XY: 0.0000248 AC XY: 18AN XY: 727020
GnomAD4 genome AF: 0.000184 AC: 28AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.823C>T (p.R275W) alteration is located in exon 7 (coding exon 7) of the PDLIM1 gene. This alteration results from a C to T substitution at nucleotide position 823, causing the arginine (R) at amino acid position 275 to be replaced by a tryptophan (W). 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