chr16-30005333-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_173618.3(INO80E):c.626C>T(p.Pro209Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000253 in 355,088 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 25)
Exomes 𝑓: 0.000025 ( 0 hom. )
Consequence
INO80E
NM_173618.3 missense
NM_173618.3 missense
Scores
5
13
Clinical Significance
Conservation
PhyloP100: 3.50
Genes affected
INO80E (HGNC:26905): (INO80 complex subunit E) Predicted to be involved in DNA recombination; DNA repair; and chromatin remodeling. Located in nucleolus and nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3366515).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
INO80E | NM_173618.3 | c.626C>T | p.Pro209Leu | missense_variant | 7/7 | ENST00000563197.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
INO80E | ENST00000563197.6 | c.626C>T | p.Pro209Leu | missense_variant | 7/7 | 1 | NM_173618.3 | P3 |
Frequencies
GnomAD3 genomes Cov.: 25
GnomAD3 genomes
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25
GnomAD3 exomes AF: 0.0000507 AC: 4AN: 78894Hom.: 0 AF XY: 0.0000911 AC XY: 4AN XY: 43930
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GnomAD4 exome AF: 0.0000253 AC: 9AN: 355088Hom.: 0 Cov.: 8 AF XY: 0.0000220 AC XY: 4AN XY: 181990
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GnomAD4 genome Cov.: 25
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2022 | The c.626C>T (p.P209L) alteration is located in exon 7 (coding exon 7) of the INO80E gene. This alteration results from a C to T substitution at nucleotide position 626, causing the proline (P) at amino acid position 209 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D;D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N
Sift
Uncertain
D;D;D
Sift4G
Benign
T;D;T
Polyphen
D;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at