X-153930079-CACT-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM1PM4_SupportingBS2
The NM_003491.4(NAA10):c.613_615delAGT(p.Ser205del) variant causes a conservative inframe deletion change. The variant allele was found at a frequency of 0.0000124 in 1,208,894 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003491.4 conservative_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NAA10 | NM_003491.4 | c.613_615delAGT | p.Ser205del | conservative_inframe_deletion | Exon 8 of 8 | ENST00000464845.6 | NP_003482.1 | |
NAA10 | NM_001256120.2 | c.595_597delAGT | p.Ser199del | conservative_inframe_deletion | Exon 8 of 8 | NP_001243049.1 | ||
NAA10 | NM_001256119.2 | c.568_570delAGT | p.Ser190del | conservative_inframe_deletion | Exon 7 of 7 | NP_001243048.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000903 AC: 1AN: 110779Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32949
GnomAD4 exome AF: 0.0000127 AC: 14AN: 1098115Hom.: 0 AF XY: 0.0000110 AC XY: 4AN XY: 363473
GnomAD4 genome AF: 0.00000903 AC: 1AN: 110779Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 32949
ClinVar
Submissions by phenotype
not provided Uncertain:1
The c.613_615delAGT variant in the NAA10 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.613_615delAGT variant causes an in-frame deletion of one amino acid residue that is not conserved across species, denoted p.S205del. The c.613_615delAGT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.613_615delAGT as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at