Variant 5-170252350-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000524171.5(C5orf58):c.*695C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 733,698 control chromosomes in the GnomAD database, including 88,359 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 15311 hom., cov: 32)

Exomes 𝑓: 0.50 ( 73048 hom. )

Consequence

C5orf58
ENST00000524171.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.45

Variant links:

Genes affected

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

C5orf58 links:

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 5-170252350-C-T is Benign according to our data. Variant chr5-170252350-C-T is described in ClinVar as [Benign]. Clinvar id is 2688122.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
LCP2	NM_005565.5 linkuse as main transcript	c.1323+84G>A	intron_variant		ENST00000046794.10	NP_005556.1
LCP2	XM_047417171.1 linkuse as main transcript	c.1092+84G>A	intron_variant			XP_047273127.1
C5orf58	NR_131091.3 linkuse as main transcript	n.904C>T	non_coding_transcript_exon_variant	4/4
C5orf58	NR_131092.3 linkuse as main transcript	n.820C>T	non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
C5orf58	ENST00000524171.5 linkuse as main transcript	c.*695C>T	3_prime_UTR_variant	4/4	1		ENSP00000490552
LCP2	ENST00000046794.10 linkuse as main transcript	c.1323+84G>A	intron_variant		1	NM_005565.5	ENSP00000046794	P1
LCP2	ENST00000521416.5 linkuse as main transcript	c.708+84G>A	intron_variant		2		ENSP00000428871

Frequencies

GnomAD3 genomes

AF:

0.433

AC:

65820

AN:

151894

Hom.:

15295

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.609

Gnomad AMR

AF:

0.460

Gnomad ASJ

AF:

0.482

Gnomad EAS

AF:

0.400

Gnomad SAS

AF:

0.535

Gnomad FIN

AF:

0.412

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.517

Gnomad OTH

AF:

0.452

GnomAD4 exome

AF:

0.496

AC:

288588

AN:

581686

Hom.:

73048

Cov.:

AF XY:

0.499

AC XY:

153363

AN XY:

307148

show subpopulations

Gnomad4 AFR exome

AF:

0.268

Gnomad4 AMR exome

AF:

0.460

Gnomad4 ASJ exome

AF:

0.485

Gnomad4 EAS exome

AF:

0.415

Gnomad4 SAS exome

AF:

0.533

Gnomad4 FIN exome

AF:

0.429

Gnomad4 NFE exome

AF:

0.519

Gnomad4 OTH exome

AF:

0.483

GnomAD4 genome

AF:

0.433

AC:

65872

AN:

152012

Hom.:

15311

Cov.:

AF XY:

0.429

AC XY:

31914

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.274

Gnomad4 AMR

AF:

0.460

Gnomad4 ASJ

AF:

0.482

Gnomad4 EAS

AF:

0.400

Gnomad4 SAS

AF:

0.534

Gnomad4 FIN

AF:

0.412

Gnomad4 NFE

AF:

0.517

Gnomad4 OTH

AF:

0.458

Alfa

AF:

0.467

Hom.:

3310

Bravo

AF:

0.430

Asia WGS

AF:

0.490

AC:

1706

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 51% of patients studied by a panel of primary immunodeficiencies. Number of patients: 48. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

8.3

DANN

Benign

0.34

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