rs10492452

Positions:

• chr13-46147427-C-A

Variant summary

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

The NM_002298.5(LCP1):​c.979-324G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,064 control chromosomes in the GnomAD database, including 2,514 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 0.16 (2514 hom., cov: 32)
• Consequence: LCP1 NM_002298.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936

Genes affected

LCP1 (HGNC:6528): (lymphocyte cytosolic protein 1) Plastins are a family of actin-binding proteins that are conserved throughout eukaryote evolution and expressed in most tissues of higher eukaryotes. In humans, two ubiquitous plastin isoforms (L and T) have been identified. Plastin 1 (otherwise known as Fimbrin) is a third distinct plastin isoform which is specifically expressed at high levels in the small intestine. The L isoform is expressed only in hemopoietic cell lineages, while the T isoform has been found in all other normal cells of solid tissues that have replicative potential (fibroblasts, endothelial cells, epithelial cells, melanocytes, etc.). However, L-plastin has been found in many types of malignant human cells of non-hemopoietic origin suggesting that its expression is induced accompanying tumorigenesis in solid tissues. [provided by RefSeq, Jul 2008]

LCP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCP1	NM_002298.5	c.979-324G>T		intron_variant		ENST00000323076.7	NP_002289.2
LCP1	XM_005266374.3	c.979-324G>T		intron_variant			XP_005266431.1
LCP1	XM_047430303.1	c.979-324G>T		intron_variant			XP_047286259.1
LCP1	XM_047430304.1	c.544-324G>T		intron_variant			XP_047286260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCP1	ENST00000323076.7	c.979-324G>T		intron_variant		1	NM_002298.5	ENSP00000315757.2
LCP1	ENST00000398576.6	c.979-324G>T		intron_variant		5		ENSP00000381581.1
LCP1	ENST00000469227.5	n.533-324G>T		intron_variant		3
CPB2-AS1	ENST00000663159.1	n.470-4067C>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24574 AN: 151946 Hom.: 2510 Cov.: 32

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0268

Gnomad SAS AF: 0.0481

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.162 AC: 24583 AN: 152064 Hom.: 2514 Cov.: 32 AF XY: 0.162 AC XY: 12022 AN XY: 74322

Gnomad4 AFR AF: 0.0641

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.0272

Gnomad4 SAS AF: 0.0479

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.144

Alfa AF: 0.188 Hom.: 1418

Bravo AF: 0.161

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.93
DANN	Benign	0.51

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: rs10492452; hg19: chr13-46721562;