3-25719550-G-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_018297.4(NGLY1):c.1875C>G(p.Val625Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000253 in 1,613,786 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V625V) has been classified as Likely benign.
Frequency
Consequence
NM_018297.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152058Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251248Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135808
GnomAD4 exome AF: 0.000259 AC: 379AN: 1461610Hom.: 6 Cov.: 31 AF XY: 0.000256 AC XY: 186AN XY: 727112
GnomAD4 genome AF: 0.000191 AC: 29AN: 152176Hom.: 2 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74408
ClinVar
Submissions by phenotype
Congenital disorder of deglycosylation Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at