1-113094605-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_ModerateBP6_ModerateBS1
The NM_014813.3(LRIG2):c.660-7G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000747 in 1,607,192 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_014813.3 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIG2 | NM_014813.3 | c.660-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000361127.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIG2 | ENST00000361127.6 | c.660-7G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_014813.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152040Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247738Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134406
GnomAD4 exome AF: 0.00000412 AC: 6AN: 1455152Hom.: 0 Cov.: 31 AF XY: 0.00000415 AC XY: 3AN XY: 723326
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152040Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74264
ClinVar
Submissions by phenotype
LRIG2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 01, 2019 | 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