16-66810767-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_003905.4(NAE1):c.1040G>A(p.Arg347His) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,613,512 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003905.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NAE1 | ENST00000290810.8 | c.1040G>A | p.Arg347His | missense_variant | Exon 14 of 20 | 1 | NM_003905.4 | ENSP00000290810.3 | ||
NAE1 | ENST00000359087.8 | c.1049G>A | p.Arg350His | missense_variant | Exon 14 of 20 | 2 | ENSP00000351990.4 | |||
NAE1 | ENST00000379463.6 | c.1022G>A | p.Arg341His | missense_variant | Exon 15 of 21 | 2 | ENSP00000368776.2 | |||
NAE1 | ENST00000394074.6 | c.773G>A | p.Arg258His | missense_variant | Exon 13 of 19 | 5 | ENSP00000377637.2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251028Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135686
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461258Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 726916
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1040G>A (p.R347H) alteration is located in exon 14 (coding exon 14) of the NAE1 gene. This alteration results from a G to A substitution at nucleotide position 1040, causing the arginine (R) at amino acid position 347 to be replaced by a histidine (H). 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