rs1246772868
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001320925.4(NAA38):c.56G>C(p.Arg19Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000138 in 1,447,778 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
NAA38
NM_001320925.4 missense
NM_001320925.4 missense
Scores
2
6
8
Clinical Significance
Conservation
PhyloP100: 4.04
Publications
0 publications found
Genes affected
NAA38 (HGNC:28212): (N-alpha-acetyltransferase 38, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex. Colocalizes with polysome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001320925.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NAA38 | TSL:1 MANE Select | c.56G>C | p.Arg19Pro | missense | Exon 1 of 3 | ENSP00000460172.2 | Q9BRA0-1 | ||
| NAA38 | TSL:1 | c.16G>C | p.Gly6Arg | missense | Exon 1 of 2 | ENSP00000332103.5 | Q9BRA0-2 | ||
| NAA38 | TSL:2 | c.56G>C | p.Arg19Pro | missense | Exon 1 of 3 | ENSP00000460841.2 | I3L3Z2 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00 AC: 0AN: 234104 AF XY: 0.00
GnomAD2 exomes
AF:
AC:
0
AN:
234104
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1447778Hom.: 0 Cov.: 33 AF XY: 0.00000139 AC XY: 1AN XY: 720280 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
1447778
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
720280
show subpopulations
African (AFR)
AF:
AC:
0
AN:
32476
American (AMR)
AF:
AC:
0
AN:
40534
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
25338
East Asian (EAS)
AF:
AC:
0
AN:
39636
South Asian (SAS)
AF:
AC:
0
AN:
84342
European-Finnish (FIN)
AF:
AC:
0
AN:
52688
Middle Eastern (MID)
AF:
AC:
0
AN:
5720
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1107266
Other (OTH)
AF:
AC:
1
AN:
59778
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1
AN:
3478
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Benign
D
LIST_S2
Benign
T
M_CAP
Uncertain
D
MetaRNN
Uncertain
T
MetaSVM
Benign
T
PhyloP100
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Gain of methylation at G6 (P = 0.0182)
MVP
MPC
ClinPred
D
GERP RS
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
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