3-66380737-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_015541.3(LRIG1):c.2895G>A(p.Pro965Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000511 in 1,614,208 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_015541.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000585 AC: 89AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000947 AC: 238AN: 251390Hom.: 3 AF XY: 0.000876 AC XY: 119AN XY: 135898
GnomAD4 exome AF: 0.000503 AC: 736AN: 1461880Hom.: 9 Cov.: 33 AF XY: 0.000513 AC XY: 373AN XY: 727242
GnomAD4 genome AF: 0.000584 AC: 89AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.000725 AC XY: 54AN XY: 74490
ClinVar
Submissions by phenotype
LRIG1-related disorder Benign:1
This variant is classified as 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