18-35479342-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_194281.4(INO80C):​c.337G>A​(p.Ala113Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000644 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000046 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000066 ( 0 hom. )

Consequence

INO80C
NM_194281.4 missense

Scores

4
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.80
Variant links:
Genes affected
INO80C (HGNC:26994): (INO80 complex subunit C) Predicted to be involved in chromatin remodeling. Part of Ino80 complex and MLL1 complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0763143).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
INO80CNM_194281.4 linkc.337G>A p.Ala113Thr missense_variant Exon 3 of 5 ENST00000334598.12 NP_919257.2 Q6PI98-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
INO80CENST00000334598.12 linkc.337G>A p.Ala113Thr missense_variant Exon 3 of 5 1 NM_194281.4 ENSP00000334473.6 Q6PI98-1
ENSG00000267140ENST00000589258.1 linkc.156+18377G>A intron_variant Intron 1 of 2 3 ENSP00000467041.1 K7ENP7

Frequencies

GnomAD3 genomes
AF:
0.0000460
AC:
7
AN:
152166
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:
0.00
Gnomad SAS
AF:
0.000829
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000123
AC:
31
AN:
251330
Hom.:
0
AF XY:
0.000214
AC XY:
29
AN XY:
135828
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000544
Gnomad SAS exome
AF:
0.000915
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000176
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000664
AC:
97
AN:
1461780
Hom.:
0
Cov.:
30
AF XY:
0.000103
AC XY:
75
AN XY:
727182
show subpopulations
Gnomad4 AFR exome
AF:
0.0000896
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000846
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000126
Gnomad4 OTH exome
AF:
0.0000662
GnomAD4 genome
AF:
0.0000460
AC:
7
AN:
152166
Hom.:
0
Cov.:
32
AF XY:
0.0000673
AC XY:
5
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000829
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000756
ExAC
AF:
0.000148
AC:
18
EpiCase
AF:
0.00
EpiControl
AF:
0.000119

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 07, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.445G>A (p.A149T) alteration is located in exon 5 (coding exon 5) of the INO80C gene. This alteration results from a G to A substitution at nucleotide position 445, causing the alanine (A) at amino acid position 149 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.14
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.31
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.016
.;T;.;.
Eigen
Benign
-0.032
Eigen_PC
Benign
0.10
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Uncertain
0.88
D;D;D;D
M_CAP
Benign
0.0040
T
MetaRNN
Benign
0.076
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
2.0
M;M;.;.
PrimateAI
Uncertain
0.59
T
PROVEAN
Benign
-1.5
.;N;N;.
REVEL
Benign
0.19
Sift
Benign
0.36
.;T;T;.
Sift4G
Benign
0.30
T;T;T;T
Polyphen
0.34
B;P;.;.
Vest4
0.66
MutPred
0.28
Gain of methylation at K109 (P = 0.0579);Gain of methylation at K109 (P = 0.0579);.;.;
MVP
0.37
MPC
0.12
ClinPred
0.16
T
GERP RS
4.8
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.11
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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: rs769397614; hg19: chr18-33059306; API