Genetic Variant LCP1:c.-24-8718C>T (chr13-46168404-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002298.5(LCP1):c.-24-8718C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,092 control chromosomes in the GnomAD database, including 7,238 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 0.28 ( 7238 hom., cov: 32)

Exomes 𝑓: 0.10 ( 0 hom. )

Consequence

LCP1
NM_002298.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.00

Publications

2 publications found

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:

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ACMG classification

Classification was made for transcript

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 = 0.455 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002298.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCP1	NM_002298.5	MANE Select	c.-24-8718C>T		intron	N/A	NP_002289.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
LCP1	ENST00000323076.7	TSL:1 MANE Select	c.-24-8718C>T	intron	N/A	ENSP00000315757.2
LCP1	ENST00000398576.6	TSL:5	c.-24-8718C>T	intron	N/A	ENSP00000381581.1
LCP1	ENST00000903164.1		c.-149-7734C>T	intron	N/A	ENSP00000573223.1

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42736

AN:

151964

Hom.:

7210

Cov.:

show subpopulations

Gnomad AFR

AF:

0.460

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.304

Gnomad SAS

AF:

0.269

Gnomad FIN

AF:

0.126

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.284

GnomAD4 exome

AF:

0.100

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.100

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.282

AC:

42816

AN:

152082

Hom.:

7238

Cov.:

AF XY:

0.277

AC XY:

20624

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.460

AC:

19086

AN:

41452

American (AMR)

AF:

0.273

AC:

4179

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.245

AC:

850

AN:

3472

East Asian (EAS)

AF:

0.305

AC:

1573

AN:

5164

South Asian (SAS)

AF:

0.269

AC:

1297

AN:

4824

European-Finnish (FIN)

AF:

0.126

AC:

1338

AN:

10602

Middle Eastern (MID)

AF:

0.316

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.201

AC:

13694

AN:

67964

Other (OTH)

AF:

0.285

AC:

600

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1427

2854

4280

5707

7134

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

416

832

1248

1664

2080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.230

Hom.:

7412

Bravo

AF:

0.301

Asia WGS

AF:

0.295

AC:

1025

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.097

(source)

DANN

Benign

0.55

PhyloP100

-2.0

PromoterAI

-0.0014

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over