rs6793110

chr3-66394191-G-A

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_Moderate BP6_Very_Strong BP7 BA1

The NM_015541.3(LRIG1):c.1317C>T(p.Ser439=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 1,593,816 control chromosomes in the GnomAD database, including 50,915 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.30 (7842 hom., cov: 33)
  • Exomes 𝑓: 0.24 (43073 hom.)
• Consequence: LRIG1 NM_015541.3 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.312

Genes affected

LRIG1 (HGNC:17360): (leucine rich repeats and immunoglobulin like domains 1) Predicted to act upstream of or within several processes, including innervation; otolith morphogenesis; and sensory perception of sound. Predicted to be located in plasma membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -19 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP6: Variant 3-66394191-G-A is Benign according to our data. Variant chr3-66394191-G-A is described in ClinVar as [Benign]. Clinvar id is 403056.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=0.312 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRIG1	NM_015541.3	c.1317C>T	p.Ser439=	synonymous_variant	12/19	ENST00000273261.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRIG1	ENST00000273261.8	c.1317C>T	p.Ser439=	synonymous_variant	12/19	1	NM_015541.3	P1
LRIG1	ENST00000383703.3	c.1389C>T	p.Ser463=	synonymous_variant	13/20	1
LRIG1	ENST00000495037.1	n.333C>T		non_coding_transcript_exon_variant	4/11	2
LRIG1	ENST00000496559.6	n.699C>T		non_coding_transcript_exon_variant	5/12	2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45691 AN: 152042 Hom.: 7822 Cov.: 33

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.0722

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.276

GnomAD3 exomes AF: 0.258 AC: 59760 AN: 231390 Hom.: 8621 AF XY: 0.249 AC XY: 31067 AN XY: 124748

Gnomad AFR exome AF: 0.463

Gnomad AMR exome AF: 0.374

Gnomad ASJ exome AF: 0.141

Gnomad EAS exome AF: 0.0781

Gnomad SAS exome AF: 0.217

Gnomad FIN exome AF: 0.308

Gnomad NFE exome AF: 0.234

Gnomad OTH exome AF: 0.241

GnomAD4 exome AF: 0.237 AC: 341994 AN: 1441656 Hom.: 43073 Cov.: 33 AF XY: 0.235 AC XY: 168349 AN XY: 716058

Gnomad4 AFR exome AF: 0.462

Gnomad4 AMR exome AF: 0.371

Gnomad4 ASJ exome AF: 0.141

Gnomad4 EAS exome AF: 0.0612

Gnomad4 SAS exome AF: 0.213

Gnomad4 FIN exome AF: 0.301

Gnomad4 NFE exome AF: 0.234

Gnomad4 OTH exome AF: 0.227

GnomAD4 genome AF: 0.301 AC: 45758 AN: 152160 Hom.: 7842 Cov.: 33 AF XY: 0.300 AC XY: 22318 AN XY: 74370

Gnomad4 AFR AF: 0.461

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.0722

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.235

Gnomad4 OTH AF: 0.272

Alfa AF: 0.263 Hom.: 3871

Bravo AF: 0.309

Asia WGS AF: 0.174 AC: 607 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

LRIG1-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 18, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	1.6
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.19		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: rs6793110; hg19: chr3-66444615; COSMIC: COSV56237823;