5-170281687-G-A

Position:

• chr5-170281687-G-A

Variant summary

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

The NM_005565.5(LCP2):​c.189-5827C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,216 control chromosomes in the GnomAD database, including 1,155 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 0.12 (1155 hom., cov: 32)
• Consequence: LCP2 NM_005565.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCP2	NM_005565.5	c.189-5827C>T		intron_variant		ENST00000046794.10	NP_005556.1
LCP2	XM_047417171.1	c.189-5827C>T		intron_variant			XP_047273127.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCP2	ENST00000046794.10	c.189-5827C>T		intron_variant		1	NM_005565.5	ENSP00000046794	P1
LCP2	ENST00000519594.5	n.305-5827C>T		intron_variant, non_coding_transcript_variant		2
LCP2	ENST00000522760.5	n.307-5827C>T		intron_variant, non_coding_transcript_variant		2
LCP2	ENST00000522823.5	n.393-5827C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.116 AC: 17611 AN: 152098 Hom.: 1155 Cov.: 32

Gnomad AFR AF: 0.0745

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0453

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0888

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.116 AC: 17611 AN: 152216 Hom.: 1155 Cov.: 32 AF XY: 0.113 AC XY: 8424 AN XY: 74422

Gnomad4 AFR AF: 0.0744

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0888

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.122

Alfa AF: 0.139 Hom.: 2216

Bravo AF: 0.113

Asia WGS AF: 0.0700 AC: 247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.44

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: rs2338873; hg19: chr5-169708691;