chr16-931792-C-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001352017.2(LMF1):c.-288G>A variant causes a splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.004 in 1,286,224 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001352017.2 splice_region
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: 0.00337 AC: 513AN: 152194Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00391 AC: 501AN: 127986Hom.: 0 AF XY: 0.00381 AC XY: 267AN XY: 70072
GnomAD4 exome AF: 0.00409 AC: 4635AN: 1133912Hom.: 13 Cov.: 31 AF XY: 0.00411 AC XY: 2283AN XY: 555976
GnomAD4 genome AF: 0.00336 AC: 512AN: 152312Hom.: 2 Cov.: 33 AF XY: 0.00303 AC XY: 226AN XY: 74486
ClinVar
Submissions by phenotype
Lipase deficiency, combined Uncertain:1
- -
not specified Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at