chr13-46129007-G-A

Position:

• chr13-46129007-G-A

Variant summary

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

The ENST00000323076.7(LCP1):​c.1752-1284C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 152,112 control chromosomes in the GnomAD database, including 54,540 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 0.84 (54540 hom., cov: 31)
• Consequence: LCP1 ENST00000323076.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCP1	NM_002298.5	c.1752-1284C>T		intron_variant		ENST00000323076.7	NP_002289.2
LCP1	XM_005266374.3	c.1752-1284C>T		intron_variant			XP_005266431.1
LCP1	XM_047430303.1	c.1752-1284C>T		intron_variant			XP_047286259.1
LCP1	XM_047430304.1	c.1317-1284C>T		intron_variant			XP_047286260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCP1	ENST00000323076.7	c.1752-1284C>T		intron_variant		1	NM_002298.5	ENSP00000315757	P1
CPB2-AS1	ENST00000663159.1	n.470-22487G>A		intron_variant, non_coding_transcript_variant
LCP1	ENST00000398576.6	c.1752-1284C>T		intron_variant		5		ENSP00000381581	P1
LCP1	ENST00000674665.1	c.459-1284C>T		intron_variant				ENSP00000501964

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127813 AN: 151994 Hom.: 54520 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.899

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.841 AC: 127880 AN: 152112 Hom.: 54540 Cov.: 31 AF XY: 0.845 AC XY: 62843 AN XY: 74376

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.961

Gnomad4 FIN AF: 0.934

Gnomad4 NFE AF: 0.899

Gnomad4 OTH AF: 0.862

Alfa AF: 0.877 Hom.: 12226

Bravo AF: 0.830

Asia WGS AF: 0.901 AC: 3129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.16

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: rs7324845; hg19: chr13-46703142;