rs11097431
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1
The NM_006457.5(PDLIM5):c.837G>A(p.Gln279=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 1,612,494 control chromosomes in the GnomAD database, including 34,913 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 3648 hom., cov: 31)
Exomes 𝑓: 0.20 ( 31265 hom. )
Consequence
PDLIM5
NM_006457.5 synonymous
NM_006457.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.24
Genes affected
PDLIM5 (HGNC:17468): (PDZ and LIM domain 5) This gene encodes a member of a family of proteins that possess a 100-amino acid PDZ domain at the N terminus and one to three LIM domains at the C-terminus. This family member functions as a scaffold protein that tethers protein kinases to the Z-disk in striated muscles. It is thought to function in cardiomyocyte expansion and in restraining postsynaptic growth of excitatory synapses. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.4).
BP7
?
Synonymous conserved (PhyloP=3.24 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDLIM5 | NM_006457.5 | c.837G>A | p.Gln279= | synonymous_variant | 6/13 | ENST00000317968.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDLIM5 | ENST00000317968.9 | c.837G>A | p.Gln279= | synonymous_variant | 6/13 | 1 | NM_006457.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.213 AC: 32292AN: 151890Hom.: 3650 Cov.: 31
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GnomAD3 exomes AF: 0.177 AC: 44466AN: 251220Hom.: 4392 AF XY: 0.173 AC XY: 23482AN XY: 135782
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GnomAD4 exome AF: 0.201 AC: 293845AN: 1460486Hom.: 31265 Cov.: 32 AF XY: 0.197 AC XY: 142864AN XY: 726592
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GnomAD4 genome ? AF: 0.213 AC: 32319AN: 152008Hom.: 3648 Cov.: 31 AF XY: 0.205 AC XY: 15199AN XY: 74278
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at