12-112049014-A-G
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024953.4(NAA25):c.1729-571T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 152,082 control chromosomes in the GnomAD database, including 9,161 homozygotes. 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 0.30 ( 9161 hom., cov: 32)
Consequence
NAA25
NM_024953.4 intron
NM_024953.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0850
Genes affected
NAA25 (HGNC:25783): (N-alpha-acetyltransferase 25, NatB auxiliary subunit) This gene encodes the auxiliary subunit of the heteromeric N-terminal acetyltransferase B complex. This complex acetylates methionine residues that are followed by acidic or asparagine residues.[provided by RefSeq, Mar 2010]
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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=-0.78).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA25 | NM_024953.4 | c.1729-571T>C | intron_variant | ENST00000261745.9 | |||
LOC124903022 | XR_007063465.1 | n.1959+2403A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA25 | ENST00000261745.9 | c.1729-571T>C | intron_variant | 1 | NM_024953.4 | P1 | |||
NAA25 | ENST00000549711.5 | c.*1435+469T>C | intron_variant, NMD_transcript_variant | 1 | |||||
NAA25 | ENST00000551858.1 | c.*1816-571T>C | intron_variant, NMD_transcript_variant | 1 | |||||
NAA25 | ENST00000552527.5 | n.1741-571T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.295 AC: 44893AN: 151964Hom.: 9165 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.295 AC: 44874AN: 152082Hom.: 9161 Cov.: 32 AF XY: 0.287 AC XY: 21305AN XY: 74320
GnomAD4 genome
?
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32
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21305
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191
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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