Variant 3-120335948-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000295628.4(LRRC58):c.506A>G(p.Glu169Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00446 in 1,574,298 control chromosomes in the GnomAD database, including 26 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0046 ( 25 hom. )

Consequence

LRRC58
ENST00000295628.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 7.10

Variant links:

Genes affected

LRRC58 (HGNC:26968): (leucine rich repeat containing 58)

LRRC58 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.05185336).

BP6

Variant 3-120335948-T-C is Benign according to our data. Variant chr3-120335948-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 2654060.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 25 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LRRC58	NM_001099678.2 linkuse as main transcript	c.506A>G	p.Glu169Gly	missense_variant	2/4	ENST00000295628.4	NP_001093148.1	Q96CX6
LRRC58	XM_047447401.1 linkuse as main transcript	c.*49A>G		3_prime_UTR_variant	3/3		XP_047303357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRRC58	ENST00000295628.4 linkuse as main transcript	c.506A>G	p.Glu169Gly	missense_variant	2/4	1	NM_001099678.2	ENSP00000295628.3		Q96CX6

Frequencies

GnomAD3 genomes

AF:

0.00315

AC:

479

AN:

152032

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00128

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00111

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.00208

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00560

Gnomad OTH

AF:

0.00192

GnomAD3 exomes

AF:

0.00305

AC:

733

AN:

240514

Hom.:

AF XY:

0.00289

AC XY:

377

AN XY:

130660

show subpopulations

Gnomad AFR exome

AF:

0.00125

Gnomad AMR exome

AF:

0.00132

Gnomad ASJ exome

AF:

0.000411

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000342

Gnomad FIN exome

AF:

0.00288

Gnomad NFE exome

AF:

0.00534

Gnomad OTH exome

AF:

0.00360

GnomAD4 exome

AF:

0.00460

AC:

6548

AN:

1422148

Hom.:

Cov.:

AF XY:

0.00437

AC XY:

3101

AN XY:

708996

show subpopulations

Gnomad4 AFR exome

AF:

0.000713

Gnomad4 AMR exome

AF:

0.00131

Gnomad4 ASJ exome

AF:

0.000273

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000477

Gnomad4 FIN exome

AF:

0.00237

Gnomad4 NFE exome

AF:

0.00565

Gnomad4 OTH exome

AF:

0.00366

GnomAD4 genome

AF:

0.00315

AC:

479

AN:

152150

Hom.:

Cov.:

AF XY:

0.00286

AC XY:

213

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.00128

Gnomad4 AMR

AF:

0.00111

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000208

Gnomad4 FIN

AF:

0.00208

Gnomad4 NFE

AF:

0.00560

Gnomad4 OTH

AF:

0.00190

Alfa

AF:

0.00465

Hom.:

Bravo

AF:

0.00324

TwinsUK

AF:

0.00890

AC:

ALSPAC

AF:

0.00363

AC:

ESP6500AA

AF:

0.00168

AC:

ESP6500EA

AF:

0.00627

AC:

ExAC

AF:

0.00312

AC:

377

Asia WGS

AF:

0.000867

AC:

AN:

3476

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Dec 01, 2022

LRRC58: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.47

BayesDel_addAF

Benign

-0.041

BayesDel_noAF

Pathogenic

0.17

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.12

Eigen

Uncertain

0.64

Eigen_PC

Uncertain

0.63

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.95

M_CAP

Benign

0.077

MetaRNN

Benign

0.052

MetaSVM

Benign

-0.55

MutationAssessor

Benign

1.9

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.51

PROVEAN

Pathogenic

-4.8

REVEL

Uncertain

0.41

Sift

Uncertain

0.0060

Sift4G

Benign

0.083

Polyphen

0.95

Vest4

0.84

MVP

0.85

MPC

2.1

ClinPred

0.032

GERP RS

5.3

Varity_R

0.48

gMVP

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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