chr5-170248161-G-C

Position:

• chr5-170248161-G-C

Variant summary

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

The NM_005565.5(LCP2):​c.*536C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,260 control chromosomes in the GnomAD database, including 17,066 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 0.47 (17039 hom., cov: 32)
  • Exomes 𝑓: 0.44 (27 hom.)
• Consequence: LCP2 NM_005565.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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]

C5orf58 (HGNC:37272): (chromosome 5 open reading frame 58)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LCP2	NM_005565.5	c.*536C>G		3_prime_UTR_variant	21/21	ENST00000046794.10	NP_005556.1
LCP2	XM_047417171.1	c.*536C>G		3_prime_UTR_variant	19/19		XP_047273127.1
C5orf58	NR_131091.3	n.202-3487G>C		intron_variant, non_coding_transcript_variant
C5orf58	NR_131092.3	n.118-3487G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LCP2	ENST00000046794.10	c.*536C>G		3_prime_UTR_variant	21/21	1	NM_005565.5	ENSP00000046794	P1
C5orf58	ENST00000524171.5	c.95-3487G>C		intron_variant		1		ENSP00000490552
C5orf58	ENST00000517575.4	c.95-3487G>C		intron_variant		3		ENSP00000490661
LCP2	ENST00000520322.1	n.1622C>G		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71372 AN: 151854 Hom.: 17028 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.480

GnomAD4 exome AF: 0.441 AC: 127 AN: 288 Hom.: 27 Cov.: 0 AF XY: 0.468 AC XY: 89 AN XY: 190

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.333

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.470 AC: 71411 AN: 151972 Hom.: 17039 Cov.: 32 AF XY: 0.466 AC XY: 34643 AN XY: 74300

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.486

Alfa AF: 0.353 Hom.: 948

Bravo AF: 0.471

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.19
DANN	Benign	0.64

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: rs10039796; hg19: chr5-169675165;