Variant 5-170259003-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_005565.5(LCP2):c.958-125A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 648,196 control chromosomes in the GnomAD database, including 79,842 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 19583 hom., cov: 32)

Exomes 𝑓: 0.49 ( 60259 hom. )

Consequence

LCP2
NM_005565.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.315

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=-0.84).

BP6

Variant 5-170259003-T-C is Benign according to our data. Variant chr5-170259003-T-C is described in ClinVar as [Benign]. Clinvar id is 2688341.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCP2	NM_005565.5 linkuse as main transcript	c.958-125A>G		intron_variant		ENST00000046794.10	NP_005556.1
LCP2	XM_047417171.1 linkuse as main transcript	c.727-125A>G		intron_variant			XP_047273127.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
LCP2	ENST00000046794.10 linkuse as main transcript	c.958-125A>G	intron_variant	1	NM_005565.5	ENSP00000046794	P1
LCP2	ENST00000520344.1 linkuse as main transcript	c.259-125A>G	intron_variant	5		ENSP00000430391
LCP2	ENST00000521416.5 linkuse as main transcript	c.343-125A>G	intron_variant	2		ENSP00000428871

Frequencies

GnomAD3 genomes

AF:

0.506

AC:

76885

AN:

151944

Hom.:

19569

Cov.:

show subpopulations

Gnomad AFR

AF:

0.535

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.523

Gnomad ASJ

AF:

0.522

Gnomad EAS

AF:

0.534

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.475

Gnomad OTH

AF:

0.505

GnomAD4 exome

AF:

0.489

AC:

242600

AN:

496134

Hom.:

60259

AF XY:

0.487

AC XY:

129603

AN XY:

266376

show subpopulations

Gnomad4 AFR exome

AF:

0.537

Gnomad4 AMR exome

AF:

0.541

Gnomad4 ASJ exome

AF:

0.515

Gnomad4 EAS exome

AF:

0.518

Gnomad4 SAS exome

AF:

0.462

Gnomad4 FIN exome

AF:

0.554

Gnomad4 NFE exome

AF:

0.475

Gnomad4 OTH exome

AF:

0.497

GnomAD4 genome

AF:

0.506

AC:

76941

AN:

152062

Hom.:

19583

Cov.:

AF XY:

0.512

AC XY:

38033

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.535

Gnomad4 AMR

AF:

0.523

Gnomad4 ASJ

AF:

0.522

Gnomad4 EAS

AF:

0.534

Gnomad4 SAS

AF:

0.461

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.475

Gnomad4 OTH

AF:

0.499

Alfa

AF:

0.486

Hom.:

29590

Bravo

AF:

0.503

Asia WGS

AF:

0.462

AC:

1602

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 21% of patients studied by a panel of primary immunodeficiencies. Number of patients: 20. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.7

DANN

Benign

0.74

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

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