9-85942296-T-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_024635.4(NAA35):c.124+13T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000742 in 1,612,426 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0039 ( 5 hom., cov: 33)
Exomes 𝑓: 0.00041 ( 4 hom. )
Consequence
NAA35
NM_024635.4 intron
NM_024635.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.832
Genes affected
NAA35 (HGNC:24340): (N-alpha-acetyltransferase 35, NatC auxiliary subunit) Involved in negative regulation of apoptotic process. Located in cytosol; nucleoplasm; and plasma membrane. Part of NatC complex. Colocalizes with polysome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BP6
Variant 9-85942296-T-C is Benign according to our data. Variant chr9-85942296-T-C is described in ClinVar as [Benign]. Clinvar id is 1971704.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 601 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA35 | NM_024635.4 | c.124+13T>C | intron_variant | ENST00000361671.10 | |||
NAA35 | NM_001321881.2 | c.124+13T>C | intron_variant | ||||
NAA35 | NM_001321882.2 | c.124+13T>C | intron_variant | ||||
NAA35 | XM_005252127.5 | c.124+13T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA35 | ENST00000361671.10 | c.124+13T>C | intron_variant | 1 | NM_024635.4 | P1 | |||
NAA35 | ENST00000376040.2 | c.124+13T>C | intron_variant | 2 | |||||
NAA35 | ENST00000416045.4 | n.221+13T>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00395 AC: 601AN: 152148Hom.: 5 Cov.: 33
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GnomAD3 exomes AF: 0.00115 AC: 286AN: 249504Hom.: 2 AF XY: 0.000741 AC XY: 100AN XY: 134924
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GnomAD4 exome AF: 0.000407 AC: 595AN: 1460160Hom.: 4 Cov.: 30 AF XY: 0.000343 AC XY: 249AN XY: 726400
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GnomAD4 genome AF: 0.00395 AC: 601AN: 152266Hom.: 5 Cov.: 33 AF XY: 0.00351 AC XY: 261AN XY: 74464
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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 | Nov 22, 2023 | - - |
Computational scores
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Benign
CADD
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DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at