chr3-16271023-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138381.5(OXNAD1):c.71C>T(p.Ala24Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000366 in 1,614,158 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_138381.5 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 | UniProt |
---|---|---|---|---|---|---|---|
OXNAD1 | NM_138381.5 | c.71C>T | p.Ala24Val | missense_variant | 3/9 | ENST00000285083.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OXNAD1 | ENST00000285083.10 | c.71C>T | p.Ala24Val | missense_variant | 3/9 | 1 | NM_138381.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251394Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135860
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461856Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 18AN XY: 727230
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.71C>T (p.A24V) alteration is located in exon 3 (coding exon 1) of the OXNAD1 gene. This alteration results from a C to T substitution at nucleotide position 71, causing the alanine (A) at amino acid position 24 to be replaced by a valine (V). 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