Menu
GeneBe

3-113723456-T-C

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_025146.4(NAA50):c.231A>G(p.Leu77=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 1,612,782 control chromosomes in the GnomAD database, including 116 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0071 ( 6 hom., cov: 32)
Exomes 𝑓: 0.011 ( 110 hom. )

Consequence

NAA50
NM_025146.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.436
Variant links:
Genes affected
NAA50 (HGNC:29533): (N-alpha-acetyltransferase 50, NatE catalytic subunit) Enables H4 histone acetyltransferase activity; peptide alpha-N-acetyltransferase activity; and peptidyl-lysine acetyltransferase activity. Involved in N-terminal protein amino acid acetylation; establishment of mitotic sister chromatid cohesion; and mitotic sister chromatid cohesion, centromeric. Located in cytosol and nucleus. Part of NatA complex. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-113723456-T-C is Benign according to our data. Variant chr3-113723456-T-C is described in ClinVar as [Benign]. Clinvar id is 3041325.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.436 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 6 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAA50NM_025146.4 linkuse as main transcriptc.231A>G p.Leu77= synonymous_variant 3/5 ENST00000240922.8
NAA50NM_001308445.2 linkuse as main transcriptc.228A>G p.Leu76= synonymous_variant 3/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAA50ENST00000240922.8 linkuse as main transcriptc.231A>G p.Leu77= synonymous_variant 3/51 NM_025146.4 P4Q9GZZ1-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00709
AC:
1079
AN:
152164
Hom.:
6
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00150
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00609
Gnomad ASJ
AF:
0.00202
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00103
Gnomad FIN
AF:
0.00424
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0126
Gnomad OTH
AF:
0.00575
GnomAD3 exomes
AF:
0.00741
AC:
1855
AN:
250476
Hom.:
13
AF XY:
0.00750
AC XY:
1016
AN XY:
135398
show subpopulations
Gnomad AFR exome
AF:
0.00191
Gnomad AMR exome
AF:
0.00433
Gnomad ASJ exome
AF:
0.00348
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000720
Gnomad FIN exome
AF:
0.00442
Gnomad NFE exome
AF:
0.0130
Gnomad OTH exome
AF:
0.00835
GnomAD4 exome
AF:
0.0109
AC:
15983
AN:
1460500
Hom.:
110
Cov.:
31
AF XY:
0.0106
AC XY:
7716
AN XY:
726550
show subpopulations
Gnomad4 AFR exome
AF:
0.00141
Gnomad4 AMR exome
AF:
0.00457
Gnomad4 ASJ exome
AF:
0.00387
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00111
Gnomad4 FIN exome
AF:
0.00460
Gnomad4 NFE exome
AF:
0.0133
Gnomad4 OTH exome
AF:
0.00791
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00709
AC:
1080
AN:
152282
Hom.:
6
Cov.:
32
AF XY:
0.00648
AC XY:
483
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.00152
Gnomad4 AMR
AF:
0.00608
Gnomad4 ASJ
AF:
0.00202
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00104
Gnomad4 FIN
AF:
0.00424
Gnomad4 NFE
AF:
0.0126
Gnomad4 OTH
AF:
0.00569
Alfa
AF:
0.00864
Hom.:
4
Bravo
AF:
0.00691
Asia WGS
AF:
0.000577
AC:
2
AN:
3478

ClinVar

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

Submissions by phenotype

NAA50-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesNov 26, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
12
Dann
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs34769551; hg19: chr3-113442303; API