18-79919395-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_025078.5(SLC66A2):c.397G>A(p.Asp133Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000273 in 1,612,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025078.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151936Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248698Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135022
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460340Hom.: 0 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 726454
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151936Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74186
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.397G>A (p.D133N) alteration is located in exon 5 (coding exon 4) of the PQLC1 gene. This alteration results from a G to A substitution at nucleotide position 397, causing the aspartic acid (D) at amino acid position 133 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