chr10-209902-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_001370100.5(ZMYND11):c.130G>A(p.Val44Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Consequence
ZMYND11
NM_001370100.5 missense
NM_001370100.5 missense
Scores
1
7
9
Clinical Significance
Conservation
PhyloP100: 8.11
Genes affected
ZMYND11 (HGNC:16966): (zinc finger MYND-type containing 11) The protein encoded by this gene was first identified by its ability to bind the adenovirus E1A protein. The protein localizes to the nucleus. It functions as a transcriptional repressor, and expression of E1A inhibits this repression. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, ZMYND11
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3752646).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZMYND11 | NM_001370100.5 | c.130G>A | p.Val44Ile | missense_variant | 3/15 | ENST00000381604.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMYND11 | ENST00000381604.9 | c.130G>A | p.Val44Ile | missense_variant | 3/15 | 5 | NM_001370100.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 08, 2019 | Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Benign
T;T;T;.;T;.;T;.;.;T;.;.;.;.;.
Eigen
Uncertain
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;.;D;D;D;D;D;D;D;D;.;D;.;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;.;N;N;N;.;N;.;N;N;N;.
REVEL
Benign
Sift
Uncertain
D;T;T;T;.;T;T;T;.;T;.;D;T;T;.
Sift4G
Benign
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.98, 0.99
.;.;.;.;D;.;.;.;.;D;.;.;.;.;.
Vest4
0.25, 0.30, 0.31, 0.32, 0.29, 0.32, 0.31, 0.32, 0.28, 0.32
MutPred
Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);.;Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);Gain of methylation at K39 (P = 0.1057);.;Gain of methylation at K39 (P = 0.1057);.;
MVP
MPC
2.5
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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
Publications
No publications associated with this variant yet.