9-85942189-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_024635.4(NAA35):āc.30C>Gā(p.Asp10Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_024635.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA35 | NM_024635.4 | c.30C>G | p.Asp10Glu | missense_variant | 2/23 | ENST00000361671.10 | |
NAA35 | NM_001321881.2 | c.30C>G | p.Asp10Glu | missense_variant | 2/23 | ||
NAA35 | NM_001321882.2 | c.30C>G | p.Asp10Glu | missense_variant | 2/23 | ||
NAA35 | XM_005252127.5 | c.30C>G | p.Asp10Glu | missense_variant | 2/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA35 | ENST00000361671.10 | c.30C>G | p.Asp10Glu | missense_variant | 2/23 | 1 | NM_024635.4 | P1 | |
NAA35 | ENST00000376040.2 | c.30C>G | p.Asp10Glu | missense_variant | 2/12 | 2 | |||
NAA35 | ENST00000416045.4 | n.127C>G | non_coding_transcript_exon_variant | 2/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251390Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135862
GnomAD4 exome AF: 0.0000650 AC: 95AN: 1461818Hom.: 0 Cov.: 30 AF XY: 0.0000729 AC XY: 53AN XY: 727202
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74274
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 24, 2022 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This variant has not been reported in the literature in individuals affected with NAA35-related conditions. This variant is present in population databases (rs148048804, gnomAD 0.003%). This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 10 of the NAA35 protein (p.Asp10Glu). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at