3-66500332-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015541.3(LRIG1):c.76C>A(p.Leu26Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000149 in 1,343,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_015541.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRIG1 | ENST00000273261.8 | c.76C>A | p.Leu26Ile | missense_variant | Exon 1 of 19 | 1 | NM_015541.3 | ENSP00000273261.3 | ||
LRIG1 | ENST00000383703.3 | c.76C>A | p.Leu26Ile | missense_variant | Exon 1 of 20 | 1 | ENSP00000373208.3 | |||
LRIG1 | ENST00000498287.5 | n.171+761C>A | intron_variant | Intron 1 of 5 | 4 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000149 AC: 2AN: 1343772Hom.: 0 Cov.: 50 AF XY: 0.00000150 AC XY: 1AN XY: 665088
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at