Variant 12-58885878-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The ENST00000320743.8(LRIG3):c.1197T>A(p.Arg399=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,585,378 control chromosomes in the GnomAD database, including 10,980 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

Frequency

Genomes: 𝑓 0.17 ( 2987 hom., cov: 32)

Exomes 𝑓: 0.096 ( 7993 hom. )

Consequence

LRIG3
ENST00000320743.8 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0130

Variant links:

Genes affected

LRIG3 (HGNC:30991): (leucine rich repeats and immunoglobulin like domains 3) Predicted to act upstream of or within otolith morphogenesis. Located in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

LRIG3 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=-0.59).

BP6

Variant 12-58885878-A-T is Benign according to our data. Variant chr12-58885878-A-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.013 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
LRIG3	NM_153377.5 linkuse as main transcript	c.1197T>A	p.Arg399=	synonymous_variant	10/19	ENST00000320743.8	NP_700356.2
LRIG3	NM_001136051.3 linkuse as main transcript	c.1017T>A	p.Arg339=	synonymous_variant	10/19		NP_001129523.1
LRIG3	XM_017018790.3 linkuse as main transcript	c.1197T>A	p.Arg399=	synonymous_variant	10/14		XP_016874279.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LRIG3	ENST00000320743.8 linkuse as main transcript	c.1197T>A	p.Arg399=	synonymous_variant	10/19	1	NM_153377.5	ENSP00000326759	P1	Q6UXM1-1
LRIG3	ENST00000379141.8 linkuse as main transcript	c.1017T>A	p.Arg339=	synonymous_variant	10/19	1		ENSP00000368436		Q6UXM1-2
LRIG3	ENST00000433272.6 linkuse as main transcript	c.1197T>A	p.Arg399=	synonymous_variant, NMD_transcript_variant	10/20	1		ENSP00000413143
LRIG3	ENST00000550304.1 linkuse as main transcript			downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.165

AC:

25111

AN:

152010

Hom.:

2960

Cov.:

show subpopulations

Gnomad AFR

AF:

0.332

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.167

Gnomad ASJ

AF:

0.0565

Gnomad EAS

AF:

0.145

Gnomad SAS

AF:

0.100

Gnomad FIN

AF:

0.0951

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0888

Gnomad OTH

AF:

0.139

GnomAD3 exomes

AF:

0.119

AC:

29633

AN:

249248

Hom.:

2370

AF XY:

0.110

AC XY:

14845

AN XY:

134752

show subpopulations

Gnomad AFR exome

AF:

0.334

Gnomad AMR exome

AF:

0.173

Gnomad ASJ exome

AF:

0.0602

Gnomad EAS exome

AF:

0.140

Gnomad SAS exome

AF:

0.0915

Gnomad FIN exome

AF:

0.0977

Gnomad NFE exome

AF:

0.0861

Gnomad OTH exome

AF:

0.103

GnomAD4 exome

AF:

0.0959

AC:

137499

AN:

1433250

Hom.:

7993

Cov.:

AF XY:

0.0946

AC XY:

67467

AN XY:

712984

show subpopulations

Gnomad4 AFR exome

AF:

0.339

Gnomad4 AMR exome

AF:

0.174

Gnomad4 ASJ exome

AF:

0.0600

Gnomad4 EAS exome

AF:

0.129

Gnomad4 SAS exome

AF:

0.0904

Gnomad4 FIN exome

AF:

0.0944

Gnomad4 NFE exome

AF:

0.0852

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.166

AC:

25190

AN:

152128

Hom.:

2987

Cov.:

AF XY:

0.164

AC XY:

12178

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.332

Gnomad4 AMR

AF:

0.167

Gnomad4 ASJ

AF:

0.0565

Gnomad4 EAS

AF:

0.145

Gnomad4 SAS

AF:

0.0994

Gnomad4 FIN

AF:

0.0951

Gnomad4 NFE

AF:

0.0888

Gnomad4 OTH

AF:

0.144

Alfa

AF:

0.105

Hom.:

396

Bravo

AF:

0.175

Asia WGS

AF:

0.191

AC:

663

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

3.7

DANN

Benign

0.59

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over