chr9-85975009-A-G
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 3P and 6B. PM1PP2BP4_ModerateBS2
The NM_024635.4(NAA35):āc.559A>Gā(p.Ser187Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000753 in 1,460,762 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S187I) has been classified as Uncertain significance.
Frequency
Consequence
NM_024635.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NAA35 | NM_024635.4 | c.559A>G | p.Ser187Gly | missense_variant | 7/23 | ENST00000361671.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NAA35 | ENST00000361671.10 | c.559A>G | p.Ser187Gly | missense_variant | 7/23 | 1 | NM_024635.4 | P1 | |
NAA35 | ENST00000376040.2 | c.559A>G | p.Ser187Gly | missense_variant | 7/12 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460762Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 726732
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 19, 2023 | The c.559A>G (p.S187G) alteration is located in exon 7 (coding exon 6) of the NAA35 gene. This alteration results from a A to G substitution at nucleotide position 559, causing the serine (S) at amino acid position 187 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at