Variant 5-170262600-G-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.926+35C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.868 in 1,522,876 control chromosomes in the GnomAD database, including 575,165 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.89 ( 60647 hom., cov: 34)

Exomes 𝑓: 0.87 ( 514518 hom. )

Consequence

LCP2
NM_005565.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.324

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 5-170262600-G-C is Benign according to our data. Variant chr5-170262600-G-C is described in ClinVar as [Benign]. Clinvar id is 2688075.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LCP2	NM_005565.5 linkuse as main transcript	c.926+35C>G		intron_variant		ENST00000046794.10
LCP2	XM_047417171.1 linkuse as main transcript	c.695+35C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
LCP2	ENST00000046794.10 linkuse as main transcript	c.926+35C>G	intron_variant	1	NM_005565.5	P1
LCP2	ENST00000520344.1 linkuse as main transcript	c.227+35C>G	intron_variant	5
LCP2	ENST00000521416.5 linkuse as main transcript	c.311+35C>G	intron_variant	2

Frequencies

GnomAD3 genomes

AF:

0.891

AC:

135630

AN:

152182

Hom.:

60602

Cov.:

show subpopulations

Gnomad AFR

AF:

0.961

Gnomad AMI

AF:

0.900

Gnomad AMR

AF:

0.876

Gnomad ASJ

AF:

0.854

Gnomad EAS

AF:

0.943

Gnomad SAS

AF:

0.951

Gnomad FIN

AF:

0.837

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.854

Gnomad OTH

AF:

0.898

GnomAD3 exomes

AF:

0.883

AC:

192264

AN:

217696

Hom.:

85106

AF XY:

0.886

AC XY:

104021

AN XY:

117456

show subpopulations

Gnomad AFR exome

AF:

0.963

Gnomad AMR exome

AF:

0.890

Gnomad ASJ exome

AF:

0.857

Gnomad EAS exome

AF:

0.938

Gnomad SAS exome

AF:

0.946

Gnomad FIN exome

AF:

0.832

Gnomad NFE exome

AF:

0.857

Gnomad OTH exome

AF:

0.872

GnomAD4 exome

AF:

0.866

AC:

1186590

AN:

1370576

Hom.:

514518

Cov.:

AF XY:

0.868

AC XY:

593851

AN XY:

684028

show subpopulations

Gnomad4 AFR exome

AF:

0.969

Gnomad4 AMR exome

AF:

0.890

Gnomad4 ASJ exome

AF:

0.856

Gnomad4 EAS exome

AF:

0.932

Gnomad4 SAS exome

AF:

0.944

Gnomad4 FIN exome

AF:

0.833

Gnomad4 NFE exome

AF:

0.854

Gnomad4 OTH exome

AF:

0.877

GnomAD4 genome

AF:

0.891

AC:

135733

AN:

152300

Hom.:

60647

Cov.:

AF XY:

0.892

AC XY:

66410

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.961

Gnomad4 AMR

AF:

0.876

Gnomad4 ASJ

AF:

0.854

Gnomad4 EAS

AF:

0.943

Gnomad4 SAS

AF:

0.951

Gnomad4 FIN

AF:

0.837

Gnomad4 NFE

AF:

0.854

Gnomad4 OTH

AF:

0.899

Alfa

AF:

0.854

Hom.:

6001

Bravo

AF:

0.898

Asia WGS

AF:

0.946

AC:

3289

AN:

3478

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 100% of patients studied by a panel of primary immunodeficiencies. Number of patients: 95. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

Cadd

Benign

2.1

Dann

Benign

0.43

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