Genetic Variant NM_002298.5:c.979-324G>T (chr13-46147427-C-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.979-324G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,064 control chromosomes in the GnomAD database, including 2,514 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 0.16 ( 2514 hom., cov: 32)

Consequence

LCP1
NM_002298.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.936

Publications

4 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:

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

CPB2-AS1 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=-0.86).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.238 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.979-324G>T		intron	N/A	NP_002289.2	P13796-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
LCP1	ENST00000323076.7	TSL:1 MANE Select	c.979-324G>T	intron	N/A	ENSP00000315757.2	P13796-1
LCP1	ENST00000398576.6	TSL:5	c.979-324G>T	intron	N/A	ENSP00000381581.1	P13796-1
LCP1	ENST00000903164.1		c.979-324G>T	intron	N/A	ENSP00000573223.1

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24574

AN:

151946

Hom.:

2510

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0643

Gnomad AMI

AF:

0.283

Gnomad AMR

AF:

0.244

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.0268

Gnomad SAS

AF:

0.0481

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.204

Gnomad OTH

AF:

0.146

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

GnomAD4 genome

AF:

0.162

AC:

24583

AN:

152064

Hom.:

2514

Cov.:

AF XY:

0.162

AC XY:

12022

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.0641

AC:

2662

AN:

41508

American (AMR)

AF:

0.244

AC:

3732

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

599

AN:

3466

East Asian (EAS)

AF:

0.0272

AC:

141

AN:

5184

South Asian (SAS)

AF:

0.0479

AC:

231

AN:

4822

European-Finnish (FIN)

AF:

0.263

AC:

2765

AN:

10526

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.204

AC:

13865

AN:

67968

Other (OTH)

AF:

0.144

AC:

305

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1025

2049

3074

4098

5123

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

256

512

768

1024

1280

<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:

0.196

Hom.:

2094

Bravo

AF:

0.161

Asia WGS

AF:

0.0510

AC:

177

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.93

(source)

DANN

Benign

0.51

PhyloP100

-0.94

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over