rs2071128
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
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
NM_003491.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.480
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 -14 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_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA10 | NM_003491.4 | c.*47C>T | 3_prime_UTR_variant | 8/8 | ENST00000464845.6 | ||
NAA10 | NM_001256119.2 | c.*47C>T | 3_prime_UTR_variant | 7/7 | |||
NAA10 | NM_001256120.2 | c.*47C>T | 3_prime_UTR_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA10 | ENST00000464845.6 | c.*47C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_003491.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.155 AC: 17082AN: 110399Hom.: 1728 Cov.: 22 AF XY: 0.162 AC XY: 5271AN XY: 32629
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GnomAD3 exomes AF: 0.267 AC: 48096AN: 179935Hom.: 6639 AF XY: 0.270 AC XY: 17560AN XY: 64943
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GnomAD4 exome AF: 0.178 AC: 175675AN: 989598Hom.: 16286 Cov.: 19 AF XY: 0.201 AC XY: 59719AN XY: 296498
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GnomAD4 genome ? AF: 0.155 AC: 17078AN: 110451Hom.: 1727 Cov.: 22 AF XY: 0.161 AC XY: 5272AN XY: 32691
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 19, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at