Variant X-153929940-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003491.4(NAA10):c.*47C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 1,100,049 control chromosomes in the GnomAD database, including 18,013 homozygotes. There are 64,991 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 1727 hom., 5272 hem., cov: 22)

Exomes 𝑓: 0.18 ( 16286 hom. 59719 hem. )

Consequence

NAA10
NM_003491.4 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.480

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant X-153929940-G-A is Benign according to our data. Variant chrX-153929940-G-A is described in ClinVar as [Benign]. Clinvar id is 1244939.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
NAA10	NM_003491.4 linkuse as main transcript	c.*47C>T	3_prime_UTR_variant	8/8	ENST00000464845.6	NP_003482.1
NAA10	NM_001256119.2 linkuse as main transcript	c.*47C>T	3_prime_UTR_variant	7/7		NP_001243048.1
NAA10	NM_001256120.2 linkuse as main transcript	c.*47C>T	3_prime_UTR_variant	8/8		NP_001243049.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAA10	ENST00000464845.6 linkuse as main transcript	c.*47C>T		3_prime_UTR_variant	8/8	1	NM_003491.4	ENSP00000417763	P1	P41227-1

Frequencies

GnomAD3 genomes

AF:

0.155

AC:

17082

AN:

110399

Hom.:

1728

Cov.:

AF XY:

0.162

AC XY:

5271

AN XY:

32629

show subpopulations

Gnomad AFR

AF:

0.0438

Gnomad AMI

AF:

0.00588

Gnomad AMR

AF:

0.358

Gnomad ASJ

AF:

0.237

Gnomad EAS

AF:

0.668

Gnomad SAS

AF:

0.520

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.275

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.211

GnomAD3 exomes

AF:

0.267

AC:

48096

AN:

179935

Hom.:

6639

AF XY:

0.270

AC XY:

17560

AN XY:

64943

show subpopulations

Gnomad AFR exome

AF:

0.0445

Gnomad AMR exome

AF:

0.487

Gnomad ASJ exome

AF:

0.258

Gnomad EAS exome

AF:

0.682

Gnomad SAS exome

AF:

0.526

Gnomad FIN exome

AF:

0.110

Gnomad NFE exome

AF:

0.130

Gnomad OTH exome

AF:

0.251

GnomAD4 exome

AF:

0.178

AC:

175675

AN:

989598

Hom.:

16286

Cov.:

AF XY:

0.201

AC XY:

59719

AN XY:

296498

show subpopulations

Gnomad4 AFR exome

AF:

0.0409

Gnomad4 AMR exome

AF:

0.477

Gnomad4 ASJ exome

AF:

0.266

Gnomad4 EAS exome

AF:

0.661

Gnomad4 SAS exome

AF:

0.519

Gnomad4 FIN exome

AF:

0.113

Gnomad4 NFE exome

AF:

0.123

Gnomad4 OTH exome

AF:

0.217

GnomAD4 genome

AF:

0.155

AC:

17078

AN:

110451

Hom.:

1727

Cov.:

AF XY:

0.161

AC XY:

5272

AN XY:

32691

show subpopulations

Gnomad4 AFR

AF:

0.0437

Gnomad4 AMR

AF:

0.359

Gnomad4 ASJ

AF:

0.237

Gnomad4 EAS

AF:

0.668

Gnomad4 SAS

AF:

0.517

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.130

Gnomad4 OTH

AF:

0.212

Alfa

AF:

0.129

Hom.:

2200

Bravo

AF:

0.175

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.5

DANN

Benign

0.84

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over