chr9-85942225-G-A
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_024635.4(NAA35):c.66G>A(p.Met22Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,614,020 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: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
NAA35
NM_024635.4 missense
NM_024635.4 missense
Scores
6
13
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.04
Genes affected
NAA35 (HGNC:24340): (N-alpha-acetyltransferase 35, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytosol; nucleoplasm; and plasma membrane. Part of NatC complex. Colocalizes with polysome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PP2
Missense variant where missense usually causes diseases, NAA35
BP4
Computational evidence support a benign effect (MetaRNN=0.07641083).
BS2
High AC in GnomAdExome4 at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA35 | NM_024635.4 | c.66G>A | p.Met22Ile | missense_variant | 2/23 | ENST00000361671.10 | |
NAA35 | NM_001321881.2 | c.66G>A | p.Met22Ile | missense_variant | 2/23 | ||
NAA35 | NM_001321882.2 | c.66G>A | p.Met22Ile | missense_variant | 2/23 | ||
NAA35 | XM_005252127.5 | c.66G>A | p.Met22Ile | missense_variant | 2/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA35 | ENST00000361671.10 | c.66G>A | p.Met22Ile | missense_variant | 2/23 | 1 | NM_024635.4 | P1 | |
NAA35 | ENST00000376040.2 | c.66G>A | p.Met22Ile | missense_variant | 2/12 | 2 | |||
NAA35 | ENST00000416045.4 | n.163G>A | non_coding_transcript_exon_variant | 2/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251446Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135892
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GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461854Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727226
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152166Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74344
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Gain of methylation at K21 (P = 0.0275);Gain of methylation at K21 (P = 0.0275);
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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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