4-94575764-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_006457.5(PDLIM5):c.440C>T(p.Ser147Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000328 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006457.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDLIM5 | NM_006457.5 | c.440C>T | p.Ser147Leu | missense_variant | Exon 5 of 13 | ENST00000317968.9 | NP_006448.5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251370Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135840
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.0000371 AC XY: 27AN XY: 727234
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.440C>T (p.S147L) alteration is located in exon 5 (coding exon 4) of the PDLIM5 gene. This alteration results from a C to T substitution at nucleotide position 440, causing the serine (S) at amino acid position 147 to be replaced by a leucine (L). 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