rs13078828
Positions:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBS1BS2
The NM_015541.3(LRIG1):c.366-11797C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0261 in 152,326 control chromosomes in the GnomAD database, including 87 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.026 ( 87 hom., cov: 33)
Consequence
LRIG1
NM_015541.3 intron
NM_015541.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.61
Genes affected
LRIG1 (HGNC:17360): (leucine rich repeats and immunoglobulin like domains 1) Predicted to act upstream of or within several processes, including innervation; otolith morphogenesis; and sensory perception of sound. Predicted to be located in plasma membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0261 (3977/152326) while in subpopulation NFE AF= 0.0424 (2884/68022). AF 95% confidence interval is 0.0411. There are 87 homozygotes in gnomad4. There are 1882 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 3977 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRIG1 | NM_015541.3 | c.366-11797C>T | intron_variant | ENST00000273261.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIG1 | ENST00000273261.8 | c.366-11797C>T | intron_variant | 1 | NM_015541.3 | P1 | |||
LRIG1 | ENST00000383703.3 | c.366-11797C>T | intron_variant | 1 | |||||
LRIG1 | ENST00000475366.5 | n.261-11797C>T | intron_variant, non_coding_transcript_variant | 4 | |||||
LRIG1 | ENST00000498287.5 | n.319-11797C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0262 AC: 3981AN: 152208Hom.: 88 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0261 AC: 3977AN: 152326Hom.: 87 Cov.: 33 AF XY: 0.0253 AC XY: 1882AN XY: 74494
GnomAD4 genome
?
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152326
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33
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1882
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74494
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8
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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