Variant chrX-153931677-C-T details in Genebe, Genetics Data Aggregator

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

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]

NAA10 links:

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]

ARHGAP4 links:

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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	Effect	MANE
NAA10	NM_003491.4 linkuse as main transcript	c.386+394G>A	intron_variant	ENST00000464845.6
NAA10	NM_001256119.2 linkuse as main transcript	c.341+639G>A	intron_variant
NAA10	NM_001256120.2 linkuse as main transcript	c.368+394G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NAA10	ENST00000464845.6 linkuse as main transcript	c.386+394G>A		intron_variant		1	NM_003491.4	P1	P41227-1

Frequencies

GnomAD3 genomes

AF:

0.393

AC:

43885

AN:

111711

Hom.:

8290

Cov.:

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.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over