7-45081858-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001146334.2(NACAD):c.4082G>A(p.Arg1361Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,545,542 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1361P) has been classified as Uncertain significance.
Frequency
Consequence
NM_001146334.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NACAD | NM_001146334.2 | c.4082G>A | p.Arg1361Gln | missense_variant | 3/8 | ENST00000490531.3 | |
NACAD | XM_006715674.4 | c.3443G>A | p.Arg1148Gln | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NACAD | ENST00000490531.3 | c.4082G>A | p.Arg1361Gln | missense_variant | 3/8 | 5 | NM_001146334.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152062Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000265 AC: 4AN: 150890Hom.: 0 AF XY: 0.0000249 AC XY: 2AN XY: 80368
GnomAD4 exome AF: 0.0000294 AC: 41AN: 1393480Hom.: 0 Cov.: 33 AF XY: 0.0000320 AC XY: 22AN XY: 687522
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152062Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 16, 2023 | The c.4082G>A (p.R1361Q) alteration is located in exon 3 (coding exon 3) of the NACAD gene. This alteration results from a G to A substitution at nucleotide position 4082, causing the arginine (R) at amino acid position 1361 to be replaced by a glutamine (Q). 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