chr7-45082243-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001146334.2(NACAD):āc.3937A>Cā(p.Met1313Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,548,810 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 (ā ).
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.3937A>C | p.Met1313Leu | missense_variant | 2/8 | ENST00000490531.3 | |
NACAD | XM_006715674.4 | c.3298A>C | p.Met1100Leu | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NACAD | ENST00000490531.3 | c.3937A>C | p.Met1313Leu | missense_variant | 2/8 | 5 | NM_001146334.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000197 AC: 3AN: 152640Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 80884
GnomAD4 exome AF: 0.00000716 AC: 10AN: 1396674Hom.: 0 Cov.: 33 AF XY: 0.00000290 AC XY: 2AN XY: 688690
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152136Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 22, 2022 | The c.3937A>C (p.M1313L) alteration is located in exon 2 (coding exon 2) of the NACAD gene. This alteration results from a A to C substitution at nucleotide position 3937, causing the methionine (M) at amino acid position 1313 to be replaced by a leucine (L). 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