rs11188256

Positions:

• chr10-95277821-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020992.4(PDLIM1):​c.97-6037A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,162 control chromosomes in the GnomAD database, including 3,333 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 0.20 (3333 hom., cov: 32)
• Consequence: PDLIM1 NM_020992.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

Genes affected

PDLIM1 (HGNC:2067): (PDZ and LIM domain 1) This gene encodes a member of the enigma protein family. The protein contains two protein interacting domains, a PDZ domain at the amino terminal end and one to three LIM domains at the carboxyl terminal. It is a cytoplasmic protein associated with the cytoskeleton. The protein may function as an adapter to bring other LIM-interacting proteins to the cytoskeleton. Pseudogenes associated with this gene are located on chromosomes 3, 14 and 17. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDLIM1	NM_020992.4	c.97-6037A>G		intron_variant		ENST00000329399.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDLIM1	ENST00000329399.7	c.97-6037A>G		intron_variant		1	NM_020992.4	P1
PDLIM1	ENST00000477757.5	n.194-8959A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29784 AN: 152044 Hom.: 3338 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.218

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.196 AC: 29802 AN: 152162 Hom.: 3333 Cov.: 32 AF XY: 0.197 AC XY: 14669 AN XY: 74382

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.217

Alfa AF: 0.217 Hom.: 3777

Bravo AF: 0.195

Asia WGS AF: 0.248 AC: 867 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	1.0
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs11188256; hg19: chr10-97037578;