X-153931677-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003491.4(NAA10):​c.386+394G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 885,635 control chromosomes in the GnomAD database, including 26,364 homozygotes. There are 65,388 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.39 ( 8296 hom., 13255 hem., cov: 24)
Exomes 𝑓: 0.22 ( 18068 hom. 52133 hem. )

Consequence

NAA10
NM_003491.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.186
Variant links:
Genes affected
NAA10 (HGNC:18704): (N-alpha-acetyltransferase 10, NatA catalytic subunit) N-alpha-acetylation is among the most common post-translational protein modifications in eukaryotic cells. This process involves the transfer of an acetyl group from acetyl-coenzyme A to the alpha-amino group on a nascent polypeptide and is essential for normal cell function. This gene encodes an N-terminal acetyltransferase that functions as the catalytic subunit of the major amino-terminal acetyltransferase A complex. Mutations in this gene are the cause of Ogden syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
ARHGAP4 (HGNC:674): (Rho GTPase activating protein 4) This gene encodes a member of the rhoGAP family of proteins which play a role in the regulation of small GTP-binding proteins belonging to the RAS superfamily. The protein encoded by the orthologous gene in rat is localized to the Golgi complex and can redistribute to microtubules. The rat protein stimulates the activity of some Rho GTPases in vitro. Genomic deletions of this gene and a neighboring gene have been found in patients with nephrogenic diabetes insipidus. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NAA10NM_003491.4 linkuse as main transcriptc.386+394G>A intron_variant ENST00000464845.6
NAA10NM_001256119.2 linkuse as main transcriptc.341+639G>A intron_variant
NAA10NM_001256120.2 linkuse as main transcriptc.368+394G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NAA10ENST00000464845.6 linkuse as main transcriptc.386+394G>A intron_variant 1 NM_003491.4 P1P41227-1

Frequencies

GnomAD3 genomes
AF:
0.393
AC:
43885
AN:
111711
Hom.:
8290
Cov.:
24
AF XY:
0.390
AC XY:
13207
AN XY:
33907
show subpopulations
Gnomad AFR
AF:
0.702
Gnomad AMI
AF:
0.0364
Gnomad AMR
AF:
0.504
Gnomad ASJ
AF:
0.268
Gnomad EAS
AF:
0.712
Gnomad SAS
AF:
0.581
Gnomad FIN
AF:
0.193
Gnomad MID
AF:
0.372
Gnomad NFE
AF:
0.194
Gnomad OTH
AF:
0.423
GnomAD4 exome
AF:
0.224
AC:
173051
AN:
773871
Hom.:
18068
Cov.:
30
AF XY:
0.228
AC XY:
52133
AN XY:
228605
show subpopulations
Gnomad4 AFR exome
AF:
0.718
Gnomad4 AMR exome
AF:
0.568
Gnomad4 ASJ exome
AF:
0.293
Gnomad4 EAS exome
AF:
0.716
Gnomad4 SAS exome
AF:
0.561
Gnomad4 FIN exome
AF:
0.178
Gnomad4 NFE exome
AF:
0.182
Gnomad4 OTH exome
AF:
0.297
GnomAD4 genome
AF:
0.393
AC:
43942
AN:
111764
Hom.:
8296
Cov.:
24
AF XY:
0.390
AC XY:
13255
AN XY:
33970
show subpopulations
Gnomad4 AFR
AF:
0.703
Gnomad4 AMR
AF:
0.504
Gnomad4 ASJ
AF:
0.268
Gnomad4 EAS
AF:
0.712
Gnomad4 SAS
AF:
0.578
Gnomad4 FIN
AF:
0.193
Gnomad4 NFE
AF:
0.194
Gnomad4 OTH
AF:
0.433
Alfa
AF:
0.281
Hom.:
6406
Bravo
AF:
0.434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.46
DANN
Benign
0.56
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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: rs1557501; hg19: chrX-153197130; API