19-8371150-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_139314.3(ANGPTL4):c.756C>T(p.His252His) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,613,780 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_139314.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000149 AC: 37AN: 249012Hom.: 0 AF XY: 0.000178 AC XY: 24AN XY: 134908
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461466Hom.: 0 Cov.: 31 AF XY: 0.0000578 AC XY: 42AN XY: 726992
GnomAD4 genome AF: 0.000105 AC: 16AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at