rs2438146

Variant summary

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

The NM_006457.5(PDLIM5):​c.96+18853C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,978 control chromosomes in the GnomAD database, including 11,187 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 ( 11187 hom., cov: 32)

Consequence

PDLIM5
NM_006457.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.313
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=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PDLIM5NM_006457.5 linkuse as main transcriptc.96+18853C>T intron_variant ENST00000317968.9 NP_006448.5 Q96HC4-1A0A024RDE8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PDLIM5ENST00000317968.9 linkuse as main transcriptc.96+18853C>T intron_variant 1 NM_006457.5 ENSP00000321746.4 Q96HC4-1

Frequencies

GnomAD3 genomes
AF:
0.372
AC:
56511
AN:
151860
Hom.:
11184
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.276
Gnomad AMI
AF:
0.502
Gnomad AMR
AF:
0.341
Gnomad ASJ
AF:
0.420
Gnomad EAS
AF:
0.180
Gnomad SAS
AF:
0.213
Gnomad FIN
AF:
0.398
Gnomad MID
AF:
0.420
Gnomad NFE
AF:
0.454
Gnomad OTH
AF:
0.423
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.372
AC:
56530
AN:
151978
Hom.:
11187
Cov.:
32
AF XY:
0.365
AC XY:
27125
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.275
Gnomad4 AMR
AF:
0.340
Gnomad4 ASJ
AF:
0.420
Gnomad4 EAS
AF:
0.181
Gnomad4 SAS
AF:
0.213
Gnomad4 FIN
AF:
0.398
Gnomad4 NFE
AF:
0.454
Gnomad4 OTH
AF:
0.419
Alfa
AF:
0.422
Hom.:
6671
Bravo
AF:
0.361
Asia WGS
AF:
0.189
AC:
654
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.94
DANN
Benign
0.70

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: rs2438146; hg19: chr4-95395388; COSMIC: COSV58752018; API