Variant chr13-46142283-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_002298.5(LCP1):c.1502+9G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0113 in 1,612,840 control chromosomes in the GnomAD database, including 149 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0077 ( 5 hom., cov: 32)

Exomes 𝑓: 0.012 ( 144 hom. )

Consequence

LCP1
NM_002298.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.498

Variant links:

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 links:

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

CPB2-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 13-46142283-C-A is Benign according to our data. Variant chr13-46142283-C-A is described in ClinVar as [Benign]. Clinvar id is 790278.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High AC in GnomAd4 at 1165 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
LCP1	NM_002298.5 linkuse as main transcript	c.1502+9G>T	intron_variant	ENST00000323076.7
LCP1	XM_005266374.3 linkuse as main transcript	c.1502+9G>T	intron_variant
LCP1	XM_047430303.1 linkuse as main transcript	c.1502+9G>T	intron_variant
LCP1	XM_047430304.1 linkuse as main transcript	c.1067+9G>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
LCP1	ENST00000323076.7 linkuse as main transcript	c.1502+9G>T	intron_variant	1	NM_002298.5	P1	P13796-1
CPB2-AS1	ENST00000663159.1 linkuse as main transcript	n.470-9211C>A	intron_variant, non_coding_transcript_variant
LCP1	ENST00000398576.6 linkuse as main transcript	c.1502+9G>T	intron_variant	5		P1	P13796-1
LCP1	ENST00000674665.1 linkuse as main transcript	c.209+9G>T	intron_variant				P13796-2

Frequencies

GnomAD3 genomes

AF:

0.00766

AC:

1165

AN:

152140

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00237

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00367

Gnomad ASJ

AF:

0.00519

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00414

Gnomad FIN

AF:

0.00387

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0133

Gnomad OTH

AF:

0.0120

GnomAD3 exomes

AF:

0.00662

AC:

1664

AN:

251360

Hom.:

AF XY:

0.00679

AC XY:

922

AN XY:

135852

show subpopulations

Gnomad AFR exome

AF:

0.00135

Gnomad AMR exome

AF:

0.00286

Gnomad ASJ exome

AF:

0.00714

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00408

Gnomad FIN exome

AF:

0.00439

Gnomad NFE exome

AF:

0.0106

Gnomad OTH exome

AF:

0.00652

GnomAD4 exome

AF:

0.0117

AC:

17050

AN:

1460582

Hom.:

144

Cov.:

AF XY:

0.0114

AC XY:

8309

AN XY:

726558

show subpopulations

Gnomad4 AFR exome

AF:

0.00170

Gnomad4 AMR exome

AF:

0.00313

Gnomad4 ASJ exome

AF:

0.00663

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00408

Gnomad4 FIN exome

AF:

0.00441

Gnomad4 NFE exome

AF:

0.0139

Gnomad4 OTH exome

AF:

0.0108

GnomAD4 genome

AF:

0.00765

AC:

1165

AN:

152258

Hom.:

Cov.:

AF XY:

0.00707

AC XY:

526

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.00236

Gnomad4 AMR

AF:

0.00366

Gnomad4 ASJ

AF:

0.00519

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.00387

Gnomad4 NFE

AF:

0.0133

Gnomad4 OTH

AF:

0.0118

Alfa

AF:

0.00964

Hom.:

Bravo

AF:

0.00683

Asia WGS

AF:

0.00202

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.16

DANN

Benign

0.33

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over