rs1671021
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001031803.2(LLGL2):āc.1435T>Cā(p.Phe479Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 1,612,362 control chromosomes in the GnomAD database, including 128,083 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001031803.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LLGL2 | NM_001031803.2 | c.1435T>C | p.Phe479Leu | missense_variant | 13/26 | ENST00000392550.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LLGL2 | ENST00000392550.8 | c.1435T>C | p.Phe479Leu | missense_variant | 13/26 | 1 | NM_001031803.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.485 AC: 73674AN: 151990Hom.: 21314 Cov.: 33
GnomAD3 exomes AF: 0.361 AC: 89446AN: 247438Hom.: 18635 AF XY: 0.353 AC XY: 47307AN XY: 134148
GnomAD4 exome AF: 0.371 AC: 542153AN: 1460254Hom.: 106719 Cov.: 54 AF XY: 0.367 AC XY: 266836AN XY: 726402
GnomAD4 genome ? AF: 0.485 AC: 73779AN: 152108Hom.: 21364 Cov.: 33 AF XY: 0.474 AC XY: 35245AN XY: 74352
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at