1-89583939-A-G

Variant summary

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

The NM_001369817.2(LRRC8B):ā€‹c.1289A>Gā€‹(p.Asn430Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,614,216 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.000066 ( 0 hom., cov: 32)
Exomes š‘“: 0.00016 ( 0 hom. )

Consequence

LRRC8B
NM_001369817.2 missense

Scores

19

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0540
Variant links:
Genes affected
LRRC8B (HGNC:30692): (leucine rich repeat containing 8 VRAC subunit B) Contributes to volume-sensitive anion channel activity. Involved in anion transmembrane transport. Located in cytoplasm and plasma membrane. Is integral component of plasma membrane. Part of ion channel complex. [provided by Alliance of Genome Resources, Apr 2022]
LRRC8C-DT (HGNC:53731): (LRRC8C divergent transcript)

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=0.0055749416).
BP6
Variant 1-89583939-A-G is Benign according to our data. Variant chr1-89583939-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2356357.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 10 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LRRC8BNM_001369817.2 linkuse as main transcriptc.1289A>G p.Asn430Ser missense_variant 5/6 ENST00000330947.7
LRRC8BNM_001134476.2 linkuse as main transcriptc.1289A>G p.Asn430Ser missense_variant 7/8
LRRC8BNM_001369819.2 linkuse as main transcriptc.1289A>G p.Asn430Ser missense_variant 6/7
LRRC8BNM_015350.4 linkuse as main transcriptc.1289A>G p.Asn430Ser missense_variant 8/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LRRC8BENST00000330947.7 linkuse as main transcriptc.1289A>G p.Asn430Ser missense_variant 5/65 NM_001369817.2 P1
LRRC8C-DTENST00000655657.3 linkuse as main transcriptn.701-515T>C intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes
AF:
0.0000657
AC:
10
AN:
152226
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000770
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000215
AC:
54
AN:
250630
Hom.:
0
AF XY:
0.000229
AC XY:
31
AN XY:
135518
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000578
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000707
Gnomad SAS exome
AF:
0.000229
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000274
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000155
AC:
227
AN:
1461872
Hom.:
0
Cov.:
34
AF XY:
0.000168
AC XY:
122
AN XY:
727230
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.000112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000655
Gnomad4 SAS exome
AF:
0.000255
Gnomad4 FIN exome
AF:
0.000169
Gnomad4 NFE exome
AF:
0.000130
Gnomad4 OTH exome
AF:
0.000232
GnomAD4 genome
AF:
0.0000656
AC:
10
AN:
152344
Hom.:
0
Cov.:
32
AF XY:
0.0000805
AC XY:
6
AN XY:
74502
show subpopulations
Gnomad4 AFR
AF:
0.0000240
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000772
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000933
Hom.:
0
Bravo
AF:
0.0000756
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.000272
AC:
33
EpiCase
AF:
0.00
EpiControl
AF:
0.000296

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingAmbry GeneticsDec 03, 2021This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.047
BayesDel_addAF
Benign
-0.67
T
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.013
DANN
Benign
0.55
DEOGEN2
Benign
0.028
T;T;T;T
Eigen
Benign
-2.3
Eigen_PC
Benign
-2.2
FATHMM_MKL
Benign
0.048
N
LIST_S2
Benign
0.72
.;.;.;T
M_CAP
Benign
0.015
T
MetaRNN
Benign
0.0056
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-2.2
N;N;N;N
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.27
T
PROVEAN
Benign
1.1
.;.;N;N
REVEL
Benign
0.11
Sift
Benign
1.0
.;.;T;T
Sift4G
Benign
1.0
.;.;T;T
Polyphen
0.0
B;B;B;B
Vest4
0.040, 0.033
MVP
0.043
MPC
0.41
ClinPred
0.021
T
GERP RS
-5.7
Varity_R
0.015
gMVP
0.13

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: rs144661004; hg19: chr1-90049498; COSMIC: COSV100446673; COSMIC: COSV100446673; API