chrX-153930184-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM1BP4_StrongBP6_ModerateBS2
The NM_003491.4(NAA10):c.511G>A(p.Val171Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000339 in 1,209,432 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003491.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA10 | NM_003491.4 | c.511G>A | p.Val171Met | missense_variant | 8/8 | ENST00000464845.6 | |
NAA10 | NM_001256120.2 | c.493G>A | p.Val165Met | missense_variant | 8/8 | ||
NAA10 | NM_001256119.2 | c.466G>A | p.Val156Met | missense_variant | 7/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA10 | ENST00000464845.6 | c.511G>A | p.Val171Met | missense_variant | 8/8 | 1 | NM_003491.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000805 AC: 9AN: 111760Hom.: 0 Cov.: 22 AF XY: 0.0000885 AC XY: 3AN XY: 33902
GnomAD3 exomes AF: 0.0000887 AC: 16AN: 180381Hom.: 0 AF XY: 0.0000758 AC XY: 5AN XY: 65959
GnomAD4 exome AF: 0.0000292 AC: 32AN: 1097672Hom.: 0 Cov.: 31 AF XY: 0.0000275 AC XY: 10AN XY: 363066
GnomAD4 genome AF: 0.0000805 AC: 9AN: 111760Hom.: 0 Cov.: 22 AF XY: 0.0000885 AC XY: 3AN XY: 33902
ClinVar
Submissions by phenotype
NAA10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 10, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at