NM_002298.5:c.*1084C>A

Variant names:

• chr13-46126507-G-T
• rs11342
• NM_002298.5:c.*1084C>A

Variant summary

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

The NM_002298.5(LCP1):​c.*1084C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 232,068 control chromosomes in the GnomAD database, including 20,232 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 0.40 (12123 hom., cov: 32)
  • Exomes 𝑓: 0.45 (8109 hom.)
• Consequence: LCP1 NM_002298.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 11 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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCP1	NM_002298.5	c.*1084C>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000323076.7	NP_002289.2
LCP1	XM_005266374.3	c.*1084C>A		3_prime_UTR_variant	Exon 16 of 16		XP_005266431.1
LCP1	XM_047430303.1	c.*1084C>A		3_prime_UTR_variant	Exon 16 of 16		XP_047286259.1
LCP1	XM_047430304.1	c.*1084C>A		3_prime_UTR_variant	Exon 14 of 14		XP_047286260.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCP1	ENST00000323076.7	c.*1084C>A		3_prime_UTR_variant	Exon 16 of 16	1	NM_002298.5	ENSP00000315757.2
LCP1	ENST00000398576.6	c.*1084C>A		3_prime_UTR_variant	Exon 19 of 19	5		ENSP00000381581.1
LCP1	ENST00000674665.1	c.*1084C>A		3_prime_UTR_variant	Exon 5 of 5			ENSP00000501964.1
CPB2-AS1	ENST00000663159.1	n.470-24987G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60146 AN: 151900 Hom.: 12126 Cov.: 32

Gnomad AFR AF: 0.310

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.458

GnomAD4 exome AF: 0.446 AC: 35735 AN: 80048 Hom.: 8109 Cov.: 0 AF XY: 0.451 AC XY: 16647 AN XY: 36928

African (AFR) AF: 0.317 AC: 1215 AN: 3832

American (AMR) AF: 0.408 AC: 996 AN: 2444

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 2309 AN: 5056

East Asian (EAS) AF: 0.497 AC: 5576 AN: 11222

South Asian (SAS) AF: 0.471 AC: 327 AN: 694

European-Finnish (FIN) AF: 0.309 AC: 154 AN: 498

Middle Eastern (MID) AF: 0.540 AC: 259 AN: 480

European-Non Finnish (NFE) AF: 0.447 AC: 21957 AN: 49174

Other (OTH) AF: 0.443 AC: 2942 AN: 6648

GnomAD4 genome AF: 0.396 AC: 60159 AN: 152020 Hom.: 12123 Cov.: 32 AF XY: 0.396 AC XY: 29416 AN XY: 74316

African (AFR) AF: 0.310 AC: 12830 AN: 41442

American (AMR) AF: 0.417 AC: 6374 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1578 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2716 AN: 5162

South Asian (SAS) AF: 0.475 AC: 2292 AN: 4824

European-Finnish (FIN) AF: 0.321 AC: 3393 AN: 10562

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.434 AC: 29506 AN: 67948

Other (OTH) AF: 0.459 AC: 968 AN: 2110

Alfa AF: 0.325 Hom.: 1576

Bravo AF: 0.398

Asia WGS AF: 0.469 AC: 1627 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.3
DANN	Benign	0.86
PhyloP100		-0.22
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: rs11342; hg19: chr13-46700642; COSMIC: COSV59942843; COSMIC: COSV59942843;