chr3-66380387-T-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015541.3(LRIG1):ā€‹c.3158A>Cā€‹(p.Gln1053Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 1,614,060 control chromosomes in the GnomAD database, including 29,674 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: š‘“ 0.16 ( 2216 hom., cov: 32)
Exomes š‘“: 0.19 ( 27458 hom. )

Consequence

LRIG1
NM_015541.3 missense

Scores

2
15

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.40
Variant links:
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]
SLC25A26 (HGNC:20661): (solute carrier family 25 member 26) This gene is a member of the mitochondrial carrier family which includes nuclear-encoded transporters localized on the inner mitochondrial membranes. Members of the family transport important small molecules across the mitochondrial inner membrane. This protein is involved in the transport of S-adenosylmethionine (SAM) into the mitochondria. Mutations in this gene are associated with combined oxidative phosphorylation deficiency 28. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Apr 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=9.765923E-4).
BP6
Variant 3-66380387-T-G is Benign according to our data. Variant chr3-66380387-T-G is described in ClinVar as [Benign]. Clinvar id is 403053.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRIG1NM_015541.3 linkuse as main transcriptc.3158A>C p.Gln1053Pro missense_variant 19/19 ENST00000273261.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LRIG1ENST00000273261.8 linkuse as main transcriptc.3158A>C p.Gln1053Pro missense_variant 19/191 NM_015541.3 P1Q96JA1-1

Frequencies

GnomAD3 genomes
AF:
0.159
AC:
24171
AN:
152088
Hom.:
2217
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0950
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.120
Gnomad ASJ
AF:
0.119
Gnomad EAS
AF:
0.0617
Gnomad SAS
AF:
0.128
Gnomad FIN
AF:
0.227
Gnomad MID
AF:
0.168
Gnomad NFE
AF:
0.207
Gnomad OTH
AF:
0.152
GnomAD3 exomes
AF:
0.160
AC:
40208
AN:
251116
Hom.:
3651
AF XY:
0.162
AC XY:
22047
AN XY:
135712
show subpopulations
Gnomad AFR exome
AF:
0.0870
Gnomad AMR exome
AF:
0.0910
Gnomad ASJ exome
AF:
0.120
Gnomad EAS exome
AF:
0.0656
Gnomad SAS exome
AF:
0.125
Gnomad FIN exome
AF:
0.232
Gnomad NFE exome
AF:
0.206
Gnomad OTH exome
AF:
0.165
GnomAD4 exome
AF:
0.189
AC:
275573
AN:
1461854
Hom.:
27458
Cov.:
33
AF XY:
0.187
AC XY:
135884
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.0926
Gnomad4 AMR exome
AF:
0.0968
Gnomad4 ASJ exome
AF:
0.123
Gnomad4 EAS exome
AF:
0.0541
Gnomad4 SAS exome
AF:
0.125
Gnomad4 FIN exome
AF:
0.230
Gnomad4 NFE exome
AF:
0.206
Gnomad4 OTH exome
AF:
0.167
GnomAD4 genome
AF:
0.159
AC:
24168
AN:
152206
Hom.:
2216
Cov.:
32
AF XY:
0.157
AC XY:
11658
AN XY:
74402
show subpopulations
Gnomad4 AFR
AF:
0.0949
Gnomad4 AMR
AF:
0.120
Gnomad4 ASJ
AF:
0.119
Gnomad4 EAS
AF:
0.0615
Gnomad4 SAS
AF:
0.128
Gnomad4 FIN
AF:
0.227
Gnomad4 NFE
AF:
0.207
Gnomad4 OTH
AF:
0.150
Alfa
AF:
0.183
Hom.:
5205
Bravo
AF:
0.146
TwinsUK
AF:
0.206
AC:
765
ALSPAC
AF:
0.210
AC:
809
ESP6500AA
AF:
0.0967
AC:
426
ESP6500EA
AF:
0.201
AC:
1726
ExAC
AF:
0.162
AC:
19671
Asia WGS
AF:
0.110
AC:
383
AN:
3478
EpiCase
AF:
0.200
EpiControl
AF:
0.201

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 29, 2016Variant 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 submitterclinical testingPreventionGenetics, part of Exact SciencesOct 21, 2019This 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
AlphaMissense
Benign
0.093
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.23
CADD
Benign
21
DANN
Benign
0.97
DEOGEN2
Benign
0.12
T;.
Eigen
Benign
-0.18
Eigen_PC
Benign
-0.13
FATHMM_MKL
Uncertain
0.86
D
MetaRNN
Benign
0.00098
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.9
M;.
MutationTaster
Benign
1.0
P;P;P
PrimateAI
Benign
0.29
T
PROVEAN
Benign
-0.43
N;N
REVEL
Benign
0.21
Sift
Uncertain
0.010
D;D
Sift4G
Benign
0.15
T;T
Polyphen
0.23
B;P
Vest4
0.50
MPC
0.14
ClinPred
0.022
T
GERP RS
3.1
Varity_R
0.16
gMVP
0.37

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.

Other links and lift over

dbSNP: rs2279290; hg19: chr3-66430811; COSMIC: COSV56250492; COSMIC: COSV56250492; API