rs398053355
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Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_014813.3(LRIG2):c.2680+10_2680+11del variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 1,586,146 control chromosomes in the GnomAD database, including 558,203 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.78 ( 46745 hom., cov: 0)
Exomes 𝑓: 0.84 ( 511458 hom. )
Consequence
LRIG2
NM_014813.3 splice_region, intron
NM_014813.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.24
Genes affected
LRIG2 (HGNC:20889): (leucine rich repeats and immunoglobulin like domains 2) This gene encodes a transmembrane protein containing leucine-rich repeats and immunoglobulin-like domains. The encoded protein promotes epidermal growth factor signalling, resulting in increased proliferation. Its expression in the cytoplasm of glioma cells is correlated with poor survival. Mutations in this gene can cause urofacial syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP6
?
Variant 1-113116443-ACT-A is Benign according to our data. Variant chr1-113116443-ACT-A is described in ClinVar as [Benign]. Clinvar id is 260443.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-113116443-ACT-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIG2 | NM_014813.3 | c.2680+10_2680+11del | splice_region_variant, intron_variant | ENST00000361127.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIG2 | ENST00000361127.6 | c.2680+10_2680+11del | splice_region_variant, intron_variant | 1 | NM_014813.3 | P1 | |||
LRIG2 | ENST00000466161.1 | n.1952+10_1952+11del | splice_region_variant, intron_variant, non_coding_transcript_variant | 2 | |||||
LRIG2 | ENST00000492207.5 | n.1459+10_1459+11del | splice_region_variant, intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.776 AC: 117832AN: 151786Hom.: 46735 Cov.: 0
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GnomAD3 exomes AF: 0.839 AC: 201585AN: 240184Hom.: 85353 AF XY: 0.848 AC XY: 109983AN XY: 129684
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GnomAD4 exome AF: 0.843 AC: 1208676AN: 1434242Hom.: 511458 AF XY: 0.846 AC XY: 600608AN XY: 710096
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GnomAD4 genome ? AF: 0.776 AC: 117876AN: 151904Hom.: 46745 Cov.: 0 AF XY: 0.780 AC XY: 57916AN XY: 74284
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 21, 2022 | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at