21-14163411-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001302998.2(LIPI):c.1006+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000507 in 1,261,596 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_001302998.2 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIPI | NM_001302998.2 | c.1006+8A>G | splice_region_variant, intron_variant | ENST00000681601.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIPI | ENST00000681601.1 | c.1006+8A>G | splice_region_variant, intron_variant | NM_001302998.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000563 AC: 14AN: 248486Hom.: 0 AF XY: 0.0000447 AC XY: 6AN XY: 134232
GnomAD4 exome AF: 0.0000171 AC: 19AN: 1109478Hom.: 0 Cov.: 15 AF XY: 0.0000193 AC XY: 11AN XY: 568682
GnomAD4 genome ? AF: 0.000296 AC: 45AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74382
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 21, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at