9-85942286-G-A
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_024635.4(NAA35):c.124+3G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00218 in 1,612,966 control chromosomes in the GnomAD database, including 72 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0036 ( 12 hom., cov: 33)
Exomes 𝑓: 0.0020 ( 60 hom. )
Consequence
NAA35
NM_024635.4 splice_donor_region, intron
NM_024635.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0003768
2
Clinical Significance
Conservation
PhyloP100: 1.22
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 -8 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP6
Variant 9-85942286-G-A is Benign according to our data. Variant chr9-85942286-G-A is described in ClinVar as [Benign]. Clinvar id is 2153456.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 542 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA35 | NM_024635.4 | c.124+3G>A | splice_donor_region_variant, intron_variant | ENST00000361671.10 | |||
NAA35 | NM_001321881.2 | c.124+3G>A | splice_donor_region_variant, intron_variant | ||||
NAA35 | NM_001321882.2 | c.124+3G>A | splice_donor_region_variant, intron_variant | ||||
NAA35 | XM_005252127.5 | c.124+3G>A | splice_donor_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA35 | ENST00000361671.10 | c.124+3G>A | splice_donor_region_variant, intron_variant | 1 | NM_024635.4 | P1 | |||
NAA35 | ENST00000376040.2 | c.124+3G>A | splice_donor_region_variant, intron_variant | 2 | |||||
NAA35 | ENST00000416045.4 | n.221+3G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00356 AC: 542AN: 152178Hom.: 12 Cov.: 33
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GnomAD3 exomes AF: 0.00463 AC: 1156AN: 249896Hom.: 25 AF XY: 0.00438 AC XY: 592AN XY: 135096
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GnomAD4 exome AF: 0.00203 AC: 2971AN: 1460670Hom.: 60 Cov.: 30 AF XY: 0.00198 AC XY: 1441AN XY: 726648
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GnomAD4 genome AF: 0.00356 AC: 542AN: 152296Hom.: 12 Cov.: 33 AF XY: 0.00520 AC XY: 387AN 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 | Jan 09, 2024 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at