9-135770966-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_020822.3(KCNT1):ā€‹c.1879A>Gā€‹(p.Ile627Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000666 in 1,613,898 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: š‘“ 0.00081 ( 0 hom., cov: 34)
Exomes š‘“: 0.00065 ( 1 hom. )

Consequence

KCNT1
NM_020822.3 missense

Scores

1
4
14

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:5

Conservation

PhyloP100: 8.74
Variant links:
Genes affected
KCNT1 (HGNC:18865): (potassium sodium-activated channel subfamily T member 1) Potassium channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a sodium-activated potassium channel subunit which is thought to function in ion conductance and developmental signaling pathways. Mutations in this gene cause the early-onset epileptic disorders, malignant migrating partial seizures of infancy and autosomal dominant nocturnal frontal lobe epilepsy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.013997674).
BP6
Variant 9-135770966-A-G is Benign according to our data. Variant chr9-135770966-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 129354.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=4}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000815 (124/152226) while in subpopulation NFE AF= 0.00115 (78/67996). AF 95% confidence interval is 0.000942. There are 0 homozygotes in gnomad4. There are 70 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High AC in GnomAd4 at 124 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KCNT1NM_020822.3 linkuse as main transcriptc.1879A>G p.Ile627Val missense_variant 18/31 ENST00000371757.7 NP_065873.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KCNT1ENST00000371757.7 linkuse as main transcriptc.1879A>G p.Ile627Val missense_variant 18/311 NM_020822.3 ENSP00000360822 A2Q5JUK3-3

Frequencies

GnomAD3 genomes
AF:
0.000815
AC:
124
AN:
152108
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00115
Gnomad OTH
AF:
0.000955
GnomAD3 exomes
AF:
0.000936
AC:
234
AN:
249948
Hom.:
1
AF XY:
0.000886
AC XY:
120
AN XY:
135436
show subpopulations
Gnomad AFR exome
AF:
0.0000621
Gnomad AMR exome
AF:
0.0000290
Gnomad ASJ exome
AF:
0.00130
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00434
Gnomad NFE exome
AF:
0.00104
Gnomad OTH exome
AF:
0.00147
GnomAD4 exome
AF:
0.000651
AC:
951
AN:
1461672
Hom.:
1
Cov.:
33
AF XY:
0.000644
AC XY:
468
AN XY:
727114
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.0000895
Gnomad4 ASJ exome
AF:
0.00107
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00420
Gnomad4 NFE exome
AF:
0.000592
Gnomad4 OTH exome
AF:
0.000563
GnomAD4 genome
AF:
0.000815
AC:
124
AN:
152226
Hom.:
0
Cov.:
34
AF XY:
0.000941
AC XY:
70
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.0000653
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00377
Gnomad4 NFE
AF:
0.00115
Gnomad4 OTH
AF:
0.000945
Alfa
AF:
0.000954
Hom.:
0
Bravo
AF:
0.000359
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.000349
AC:
3
ExAC
AF:
0.000956
AC:
116
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000709
EpiControl
AF:
0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:5
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:1Benign:1
Benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2024KCNT1: BS1, BS2 -
Uncertain significance, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoJan 22, 2014- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxOct 16, 2017This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Developmental and epileptic encephalopathy, 14;C3554306:Autosomal dominant nocturnal frontal lobe epilepsy 5 Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 27, 2024- -
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitterclinical testingAmbry GeneticsJan 25, 2019This alteration is classified as 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. -
KCNT1-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesApr 20, 2020This 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
0.17
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.25
CADD
Benign
22
DANN
Uncertain
1.0
DEOGEN2
Benign
0.081
.;.;.;.;.;.;.;.;T;.
Eigen
Benign
0.074
Eigen_PC
Benign
0.18
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.94
D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
0.055
D
MetaRNN
Benign
0.014
T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.5
.;.;.;.;.;.;.;.;M;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.76
T
PROVEAN
Benign
-0.90
.;.;N;N;.;.;.;.;N;N
REVEL
Benign
0.22
Sift
Benign
0.065
.;.;T;T;.;.;.;.;T;T
Sift4G
Benign
0.076
T;T;T;T;T;T;T;T;T;T
Polyphen
0.019
.;.;.;.;.;.;.;.;B;.
Vest4
0.65
MVP
0.51
MPC
0.53
ClinPred
0.13
T
GERP RS
3.9
Varity_R
0.36
gMVP
0.51

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: rs143355299; hg19: chr9-138662812; API