rs2338871

Variant names:

• chr5-170262515-G-A
• rs2338871
• NM_005565.5:c.926+120C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-170262515-G-A
• chr5-170262515-G-C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005565.5(LCP2):​c.926+120C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 686,120 control chromosomes in the GnomAD database, including 14,527 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.17 (2597 hom., cov: 32)
  • Exomes 𝑓: 0.21 (11930 hom.)
• Consequence: LCP2 NM_005565.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.768
• Publications: 5 publications found

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 Gene-Disease associations (from GenCC):

• immunodeficiency 81

  Inheritance: AR, Unknown Classification: DEFINITIVE, LIMITED Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BP6: Variant 5-170262515-G-A is Benign according to our data. Variant chr5-170262515-G-A is described in ClinVar as Benign. ClinVar VariationId is 2688247.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005565.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCP2	NM_005565.5	MANE Select	c.926+120C>T		intron	N/A	NP_005556.1	Q13094

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LCP2	ENST00000046794.10	TSL:1 MANE Select	c.926+120C>T		intron	N/A	ENSP00000046794.5	Q13094
	LCP2	ENST00000968849.1		c.935+120C>T		intron	N/A	ENSP00000638908.1
	LCP2	ENST00000968850.1		c.842+120C>T		intron	N/A	ENSP00000638909.1

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25775 AN: 152052 Hom.: 2593 Cov.: 32

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.166

GnomAD4 exome AF: 0.205 AC: 109461 AN: 533950 Hom.: 11930 AF XY: 0.204 AC XY: 57059 AN XY: 280184

African (AFR) AF: 0.0605 AC: 827 AN: 13662

American (AMR) AF: 0.275 AC: 5252 AN: 19080

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 2018 AN: 14276

East Asian (EAS) AF: 0.290 AC: 9146 AN: 31584

South Asian (SAS) AF: 0.184 AC: 8707 AN: 47442

European-Finnish (FIN) AF: 0.209 AC: 8776 AN: 41930

Middle Eastern (MID) AF: 0.121 AC: 260 AN: 2142

European-Non Finnish (NFE) AF: 0.205 AC: 68690 AN: 335054

Other (OTH) AF: 0.201 AC: 5785 AN: 28780

GnomAD4 genome AF: 0.169 AC: 25790 AN: 152170 Hom.: 2597 Cov.: 32 AF XY: 0.173 AC XY: 12861 AN XY: 74374

African (AFR) AF: 0.0606 AC: 2519 AN: 41548

American (AMR) AF: 0.250 AC: 3812 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 493 AN: 3472

East Asian (EAS) AF: 0.305 AC: 1575 AN: 5170

South Asian (SAS) AF: 0.189 AC: 913 AN: 4824

European-Finnish (FIN) AF: 0.213 AC: 2246 AN: 10566

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13640 AN: 68002

Other (OTH) AF: 0.164 AC: 346 AN: 2116

Alfa AF: 0.192 Hom.: 5076

Bravo AF: 0.170

Asia WGS AF: 0.247 AC: 856 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.14
DANN	Benign	0.73
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2338871; hg19: chr5-169689519;