chr4-139301847-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_057175.5(NAA15):c.54+16C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000157 in 1,581,716 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 1 hom. )
Consequence
NAA15
NM_057175.5 intron
NM_057175.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.45
Genes affected
NDUFC1 (HGNC:7705): (NADH:ubiquinone oxidoreductase subunit C1) The encoded protein is a subunit of the NADH:ubiquinone oxidoreductase (complex I), the first enzyme complex in the electron transport chain located in the inner mitochondrial membrane. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
NAA15 (HGNC:30782): (N-alpha-acetyltransferase 15, NatA auxiliary 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 the auxillary subunit of the N-terminal acetyltransferase A (NatA) complex. [provided by RefSeq, Jan 2017]
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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=-0.73).
BP6
?
Variant 4-139301847-C-T is Benign according to our data. Variant chr4-139301847-C-T is described in ClinVar as [Benign]. Clinvar id is 1903314.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00023 (35/152312) while in subpopulation EAS AF= 0.00154 (8/5184). AF 95% confidence interval is 0.000768. There are 0 homozygotes in gnomad4. There are 16 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 35 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NDUFC1 | NM_001184989.2 | c.-222+569G>A | intron_variant | ENST00000394223.2 | |||
NAA15 | NM_057175.5 | c.54+16C>T | intron_variant | ENST00000296543.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA15 | ENST00000296543.10 | c.54+16C>T | intron_variant | 1 | NM_057175.5 | P3 | |||
NDUFC1 | ENST00000394223.2 | c.-222+569G>A | intron_variant | 3 | NM_001184989.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152194Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000349 AC: 70AN: 200574Hom.: 0 AF XY: 0.000321 AC XY: 35AN XY: 109164
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GnomAD4 exome AF: 0.000149 AC: 213AN: 1429404Hom.: 1 Cov.: 30 AF XY: 0.000144 AC XY: 102AN XY: 707626
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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 | Invitae | Dec 27, 2023 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at