NM_001013653.3:c.641C>G
Variant summary
Our verdict is . The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
Likely benign
The NM_001013653.3(LRRC26):c.641C>G(p.Ala214Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,264,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
LRRC26
NM_001013653.3 missense
NM_001013653.3 missense
Scores
1
18
Clinical Significance
Conservation
PhyloP100: -0.658
Publications
0 publications found
Genes affected
LRRC26 (HGNC:31409): (leucine rich repeat containing 26) Enables potassium channel activator activity; transmembrane transporter binding activity; and voltage-gated potassium channel activity. Involved in positive regulation of voltage-gated potassium channel activity and potassium ion transmembrane transport. Is integral component of plasma membrane. Part of voltage-gated potassium channel complex. [provided by Alliance of Genome Resources, Apr 2022]
ENSG00000261793 (HGNC:):
MIR3621 (HGNC:38930): (microRNA 3621) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]
Genome browser will be placed here
new If you want to explore the variant's impact on the transcript NM_001013653.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -6 ACMG points.
BP4
Computational evidence support a benign effect (REVEL=0.036).
BS2
High AC in GnomAdExome4 at 24 AD gene.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001013653.3. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LRRC26 | TSL:1 MANE Select | c.641C>G | p.Ala214Gly | missense | Exon 1 of 2 | ENSP00000360597.3 | Q2I0M4-1 | ||
| ENSG00000261793 | TSL:3 | c.*28-118C>G | intron | N/A | ENSP00000480768.1 | A0A087WX66 | |||
| MIR3621 | TSL:6 | n.-33C>G | upstream_gene | N/A |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
34
GnomAD4 exome AF: 0.0000190 AC: 24AN: 1264130Hom.: 0 Cov.: 30 AF XY: 0.0000258 AC XY: 16AN XY: 620556 show subpopulations
GnomAD4 exome
AF:
AC:
24
AN:
1264130
Hom.:
Cov.:
30
AF XY:
AC XY:
16
AN XY:
620556
show subpopulations
African (AFR)
AF:
AC:
0
AN:
24726
American (AMR)
AF:
AC:
0
AN:
15888
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20442
East Asian (EAS)
AF:
AC:
0
AN:
27536
South Asian (SAS)
AF:
AC:
1
AN:
63446
European-Finnish (FIN)
AF:
AC:
0
AN:
31538
Middle Eastern (MID)
AF:
AC:
0
AN:
3812
European-Non Finnish (NFE)
AF:
AC:
23
AN:
1024670
Other (OTH)
AF:
AC:
0
AN:
52072
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.483
Heterozygous variant carriers
0
2
4
5
7
9
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
34
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
M_CAP
Benign
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.
Publications
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Other links and lift over
dbSNP: rs556924343 ;
hg19: chr9-140063755;