chr3-66380813-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_015541.3(LRIG1):āc.2819G>Cā(p.Cys940Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,614,240 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. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C940Y) has been classified as Uncertain significance.
Frequency
Consequence
NM_015541.3 missense
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 |
---|---|---|---|---|---|---|---|
LRIG1 | NM_015541.3 | c.2819G>C | p.Cys940Ser | missense_variant | 18/19 | ENST00000273261.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRIG1 | ENST00000273261.8 | c.2819G>C | p.Cys940Ser | missense_variant | 18/19 | 1 | NM_015541.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000151 AC: 38AN: 251254Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135808
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461886Hom.: 0 Cov.: 33 AF XY: 0.0000454 AC XY: 33AN XY: 727242
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at