rs1543013

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000317968.9(PDLIM5):​c.1283+1081C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,880 control chromosomes in the GnomAD database, including 11,214 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 0.37 ( 11214 hom., cov: 32)

Consequence

PDLIM5
ENST00000317968.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0400
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.57).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PDLIM5NM_006457.5 linkuse as main transcriptc.1283+1081C>A intron_variant ENST00000317968.9 NP_006448.5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PDLIM5ENST00000317968.9 linkuse as main transcriptc.1283+1081C>A intron_variant 1 NM_006457.5 ENSP00000321746 P3Q96HC4-1

Frequencies

GnomAD3 genomes
AF:
0.367
AC:
55622
AN:
151762
Hom.:
11212
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.188
Gnomad AMI
AF:
0.492
Gnomad AMR
AF:
0.388
Gnomad ASJ
AF:
0.503
Gnomad EAS
AF:
0.402
Gnomad SAS
AF:
0.614
Gnomad FIN
AF:
0.495
Gnomad MID
AF:
0.547
Gnomad NFE
AF:
0.420
Gnomad OTH
AF:
0.375
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.366
AC:
55637
AN:
151880
Hom.:
11214
Cov.:
32
AF XY:
0.375
AC XY:
27792
AN XY:
74190
show subpopulations
Gnomad4 AFR
AF:
0.188
Gnomad4 AMR
AF:
0.388
Gnomad4 ASJ
AF:
0.503
Gnomad4 EAS
AF:
0.403
Gnomad4 SAS
AF:
0.611
Gnomad4 FIN
AF:
0.495
Gnomad4 NFE
AF:
0.420
Gnomad4 OTH
AF:
0.381
Alfa
AF:
0.257
Hom.:
682
Bravo
AF:
0.349

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.57
CADD
Benign
5.6
DANN
Benign
0.85

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1543013; hg19: chr4-95562682; API