9-137430805-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001256067.2(NOXA1):c.634G>A(p.Asp212Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000364 in 1,595,022 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001256067.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NOXA1 | NM_001256067.2 | c.634G>A | p.Asp212Asn | missense_variant | 6/14 | ENST00000683555.1 | NP_001242996.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NOXA1 | ENST00000683555.1 | c.634G>A | p.Asp212Asn | missense_variant | 6/14 | NM_001256067.2 | ENSP00000507846 | P1 | ||
NOXA1 | ENST00000341349.6 | c.634G>A | p.Asp212Asn | missense_variant | 6/14 | 1 | ENSP00000342848 | |||
NOXA1 | ENST00000392815.2 | c.505-270G>A | intron_variant | 1 | ENSP00000376562 | |||||
NOXA1 | ENST00000683683.1 | c.508G>A | p.Asp170Asn | missense_variant | 5/9 | ENSP00000506984 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152208Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.0000666 AC: 15AN: 225260Hom.: 0 AF XY: 0.0000640 AC XY: 8AN XY: 124994
GnomAD4 exome AF: 0.0000326 AC: 47AN: 1442814Hom.: 0 Cov.: 32 AF XY: 0.0000279 AC XY: 20AN XY: 717502
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152208Hom.: 1 Cov.: 34 AF XY: 0.0000807 AC XY: 6AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.634G>A (p.D212N) alteration is located in exon 6 (coding exon 6) of the NOXA1 gene. This alteration results from a G to A substitution at nucleotide position 634, causing the aspartic acid (D) at amino acid position 212 to be replaced by an asparagine (N). 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