7-45082524-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001146334.2(NACAD):c.3656C>T(p.Thr1219Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000219 in 1,549,444 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001146334.2 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 | UniProt |
---|---|---|---|---|---|---|---|
NACAD | NM_001146334.2 | c.3656C>T | p.Thr1219Met | missense_variant | 2/8 | ENST00000490531.3 | |
NACAD | XM_006715674.4 | c.3282-265C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NACAD | ENST00000490531.3 | c.3656C>T | p.Thr1219Met | missense_variant | 2/8 | 5 | NM_001146334.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000345 AC: 5AN: 145116Hom.: 0 AF XY: 0.0000129 AC XY: 1AN XY: 77756
GnomAD4 exome AF: 0.0000236 AC: 33AN: 1397348Hom.: 0 Cov.: 33 AF XY: 0.0000218 AC XY: 15AN XY: 689176
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152096Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 26, 2022 | The c.3656C>T (p.T1219M) alteration is located in exon 2 (coding exon 2) of the NACAD gene. This alteration results from a C to T substitution at nucleotide position 3656, causing the threonine (T) at amino acid position 1219 to be replaced by a methionine (M). 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