chr19-42402058-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_005357.4(LIPE):c.2985C>T(p.Pro995Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000885 in 1,504,350 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005357.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000716 AC: 109AN: 152260Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000734 AC: 79AN: 107668Hom.: 0 AF XY: 0.000808 AC XY: 47AN XY: 58184
GnomAD4 exome AF: 0.000905 AC: 1223AN: 1351972Hom.: 1 Cov.: 36 AF XY: 0.000929 AC XY: 615AN XY: 662110
GnomAD4 genome AF: 0.000715 AC: 109AN: 152378Hom.: 0 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:2
LIPE: BP4, BP7 -
- -
not specified Benign:1
- -
LIPE-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at