8-144051373-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_017570.5(OPLAH):c.3820G>A(p.Glu1274Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,607,068 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E1274V) has been classified as Likely benign.
Frequency
Consequence
NM_017570.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000198 AC: 30AN: 151598Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000221 AC: 53AN: 239718Hom.: 0 AF XY: 0.000205 AC XY: 27AN XY: 131890
GnomAD4 exome AF: 0.0000983 AC: 143AN: 1455354Hom.: 1 Cov.: 34 AF XY: 0.000127 AC XY: 92AN XY: 724152
GnomAD4 genome AF: 0.000198 AC: 30AN: 151714Hom.: 0 Cov.: 32 AF XY: 0.000202 AC XY: 15AN XY: 74140
ClinVar
Submissions by phenotype
5-Oxoprolinase deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at