rs10507236
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_024953.4(NAA25):c.2797-982A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0555 in 152,258 control chromosomes in the GnomAD database, including 1,310 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 0.056 ( 1310 hom., cov: 32)
Consequence
NAA25
NM_024953.4 intron
NM_024953.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.841
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=-0.83).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA25 | NM_024953.4 | c.2797-982A>G | intron_variant | ENST00000261745.9 | |||
NAA25 | XM_006719606.3 | c.2713-982A>G | intron_variant | ||||
NAA25 | XM_047429557.1 | c.2389-982A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA25 | ENST00000261745.9 | c.2797-982A>G | intron_variant | 1 | NM_024953.4 | P1 | |||
NAA25 | ENST00000549711.5 | c.*2504-982A>G | intron_variant, NMD_transcript_variant | 1 | |||||
NAA25 | ENST00000548181.1 | n.2174-982A>G | intron_variant, non_coding_transcript_variant | 2 | |||||
NAA25 | ENST00000552527.5 | n.3950-982A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0555 AC: 8450AN: 152140Hom.: 1315 Cov.: 32
GnomAD3 genomes
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152140
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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: 0.0555 AC: 8455AN: 152258Hom.: 1310 Cov.: 32 AF XY: 0.0620 AC XY: 4620AN XY: 74458
GnomAD4 genome
?
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8455
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152258
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32
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4620
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74458
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852
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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