rs9316187

Variant names:

• chr13-46139567-G-A
• rs9316187
• NM_002298.5:c.1502+2725C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002298.5(LCP1):​c.1502+2725C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,002 control chromosomes in the GnomAD database, including 7,266 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 0.29 (7266 hom., cov: 32)
• Consequence: LCP1 NM_002298.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0940
• Publications: 7 publications found

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]

CPB2-AS1 (HGNC:39898): (CPB2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCP1	NM_002298.5	c.1502+2725C>T		intron_variant	Intron 13 of 15	ENST00000323076.7	NP_002289.2
LCP1	XM_005266374.3	c.1502+2725C>T		intron_variant	Intron 13 of 15		XP_005266431.1
LCP1	XM_047430303.1	c.1502+2725C>T		intron_variant	Intron 13 of 15		XP_047286259.1
LCP1	XM_047430304.1	c.1067+2725C>T		intron_variant	Intron 11 of 13		XP_047286260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCP1	ENST00000323076.7	c.1502+2725C>T		intron_variant	Intron 13 of 15	1	NM_002298.5	ENSP00000315757.2
LCP1	ENST00000398576.6	c.1502+2725C>T		intron_variant	Intron 16 of 18	5		ENSP00000381581.1
LCP1	ENST00000674665.1	c.209+2725C>T		intron_variant	Intron 2 of 4			ENSP00000501964.1
CPB2-AS1	ENST00000663159.1	n.470-11927G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43372 AN: 151884 Hom.: 7241 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0694

Gnomad SAS AF: 0.0559

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.286 AC: 43448 AN: 152002 Hom.: 7266 Cov.: 32 AF XY: 0.280 AC XY: 20835 AN XY: 74314

African (AFR) AF: 0.450 AC: 18655 AN: 41440

American (AMR) AF: 0.200 AC: 3061 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3468

East Asian (EAS) AF: 0.0699 AC: 362 AN: 5176

South Asian (SAS) AF: 0.0555 AC: 268 AN: 4826

European-Finnish (FIN) AF: 0.290 AC: 3051 AN: 10520

Middle Eastern (MID) AF: 0.182 AC: 53 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16512 AN: 67966

Other (OTH) AF: 0.240 AC: 506 AN: 2110

Alfa AF: 0.245 Hom.: 2878

Bravo AF: 0.286

Asia WGS AF: 0.0990 AC: 347 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.62
PhyloP100		0.094
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9316187; hg19: chr13-46713702;