5-170263243-T-C

Position:

• chr5-170263243-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000046794.10(LCP2):​c.773-251A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 152,164 control chromosomes in the GnomAD database, including 39,163 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 0.72 (39163 hom., cov: 32)
• Consequence: LCP2 ENST00000046794.10 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.543

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCP2	NM_005565.5	c.773-251A>G		intron_variant		ENST00000046794.10	NP_005556.1
LCP2	XM_047417171.1	c.542-251A>G		intron_variant			XP_047273127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCP2	ENST00000046794.10	c.773-251A>G		intron_variant		1	NM_005565.5	ENSP00000046794	P1
LCP2	ENST00000520344.1	c.74-251A>G		intron_variant		5		ENSP00000430391
LCP2	ENST00000521416.5	c.158-251A>G		intron_variant		2		ENSP00000428871

Frequencies

GnomAD3 genomes AF: 0.716 AC: 108789 AN: 152044 Hom.: 39127 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.716 AC: 108881 AN: 152164 Hom.: 39163 Cov.: 32 AF XY: 0.719 AC XY: 53506 AN XY: 74388

Gnomad4 AFR AF: 0.702

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.697

Alfa AF: 0.704 Hom.: 49404

Bravo AF: 0.714

Asia WGS AF: 0.860 AC: 2990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.32
DANN	Benign	0.50

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

Other links and lift over

dbSNP: rs10475933; hg19: chr5-169690247;