22-43923872-C-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_025225.3(PNPLA3):c.-40C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00919 in 1,461,344 control chromosomes in the GnomAD database, including 84 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_025225.3 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00714 AC: 1086AN: 152154Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00642 AC: 495AN: 77056Hom.: 1 AF XY: 0.00661 AC XY: 284AN XY: 42992
GnomAD4 exome AF: 0.00943 AC: 12351AN: 1309080Hom.: 76 Cov.: 30 AF XY: 0.00918 AC XY: 5883AN XY: 640608
GnomAD4 genome AF: 0.00713 AC: 1086AN: 152264Hom.: 8 Cov.: 32 AF XY: 0.00706 AC XY: 526AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
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NAFLD1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at