dbSNP rs315721: LCP2:c.142-18T>C (chr5-170288034-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_005565.5(LCP2):c.142-18T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 1,611,306 control chromosomes in the GnomAD database, including 82,776 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.34 ( 8850 hom., cov: 32)

Exomes 𝑓: 0.32 ( 73926 hom. )

Consequence

LCP2
NM_005565.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0870

Variant links:

Genes affected

LCP2 (HGNC:6529): (lymphocyte cytosolic protein 2) This gene encodes an adapter protein that acts as a substrate of the T cell antigen receptor (TCR)-activated protein tyrosine kinase pathway. The encoded protein associates with growth factor receptor bound protein 2, and is thought to play a role TCR-mediated intracellular signal transduction. A similar protein in mouse plays a role in normal T-cell development and activation. Mice lacking this gene show subcutaneous and intraperitoneal fetal hemorrhaging, dysfunctional platelets and impaired viability. [provided by RefSeq, Nov 2016]

LCP2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 5-170288034-A-G is Benign according to our data. Variant chr5-170288034-A-G is described in ClinVar as [Benign]. Clinvar id is 2688081.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LCP2	NM_005565.5 link	c.142-18T>C		intron_variant	Intron 2 of 20	ENST00000046794.10	NP_005556.1	Q13094
LCP2	XM_047417171.1 link	c.142-18T>C		intron_variant	Intron 2 of 18		XP_047273127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LCP2	ENST00000046794.10 link	c.142-18T>C		intron_variant	Intron 2 of 20	1	NM_005565.5	ENSP00000046794.5		Q13094

Frequencies

GnomAD3 genomes

AF:

0.338

AC:

51403

AN:

151858

Hom.:

8837

Cov.:

show subpopulations

Gnomad AFR

AF:

0.380

Gnomad AMI

AF:

0.385

Gnomad AMR

AF:

0.341

Gnomad ASJ

AF:

0.349

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.294

Gnomad MID

AF:

0.358

Gnomad NFE

AF:

0.313

Gnomad OTH

AF:

0.344

GnomAD3 exomes

AF:

0.335

AC:

83375

AN:

248914

Hom.:

14125

AF XY:

0.335

AC XY:

45303

AN XY:

135044

show subpopulations

Gnomad AFR exome

AF:

0.376

Gnomad AMR exome

AF:

0.377

Gnomad ASJ exome

AF:

0.353

Gnomad EAS exome

AF:

0.342

Gnomad SAS exome

AF:

0.366

Gnomad FIN exome

AF:

0.281

Gnomad NFE exome

AF:

0.316

Gnomad OTH exome

AF:

0.327

GnomAD4 exome

AF:

0.315

AC:

460290

AN:

1459330

Hom.:

73926

Cov.:

AF XY:

0.317

AC XY:

230289

AN XY:

726048

show subpopulations

Gnomad4 AFR exome

AF:

0.381

Gnomad4 AMR exome

AF:

0.370

Gnomad4 ASJ exome

AF:

0.352

Gnomad4 EAS exome

AF:

0.411

Gnomad4 SAS exome

AF:

0.365

Gnomad4 FIN exome

AF:

0.289

Gnomad4 NFE exome

AF:

0.303

Gnomad4 OTH exome

AF:

0.325

GnomAD4 genome

AF:

0.339

AC:

51463

AN:

151976

Hom.:

8850

Cov.:

AF XY:

0.337

AC XY:

25058

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.380

Gnomad4 AMR

AF:

0.341

Gnomad4 ASJ

AF:

0.349

Gnomad4 EAS

AF:

0.364

Gnomad4 SAS

AF:

0.382

Gnomad4 FIN

AF:

0.294

Gnomad4 NFE

AF:

0.313

Gnomad4 OTH

AF:

0.341

Alfa

AF:

0.323

Hom.:

11293

Bravo

AF:

0.341

Asia WGS

AF:

0.350

AC:

1216

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 58% of patients studied by a panel of primary immunodeficiencies. Number of patients: 55. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.97

DANN

Benign

0.65

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