rs375877098
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6BP7BS1BS2
The NM_003491.4(NAA10):c.141C>T(p.Asp47=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 1,208,695 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003491.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA10 | NM_003491.4 | c.141C>T | p.Asp47= | synonymous_variant | 3/8 | ENST00000464845.6 | |
NAA10 | NM_001256120.2 | c.141C>T | p.Asp47= | synonymous_variant | 3/8 | ||
NAA10 | NM_001256119.2 | c.141C>T | p.Asp47= | synonymous_variant | 3/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA10 | ENST00000464845.6 | c.141C>T | p.Asp47= | synonymous_variant | 3/8 | 1 | NM_003491.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000808 AC: 9AN: 111323Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33579
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183412Hom.: 0 AF XY: 0.0000442 AC XY: 3AN XY: 67846
GnomAD4 exome AF: 0.0000365 AC: 40AN: 1097372Hom.: 0 Cov.: 29 AF XY: 0.0000386 AC XY: 14AN XY: 362758
GnomAD4 genome AF: 0.0000808 AC: 9AN: 111323Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33579
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 30, 2017 | - - |
NAA10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 14, 2019 | 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). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at