chr11-27367901-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBS2_Supporting
The NM_018490.5(LGR4):c.2822G>A(p.Arg941His) variant causes a missense change. The variant allele was found at a frequency of 0.0000399 in 1,602,236 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018490.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGR4 | ENST00000379214.9 | c.2822G>A | p.Arg941His | missense_variant | Exon 18 of 18 | 1 | NM_018490.5 | ENSP00000368516.4 | ||
LGR4 | ENST00000389858.4 | c.2750G>A | p.Arg917His | missense_variant | Exon 17 of 17 | 1 | ENSP00000374508.4 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000251 AC: 6AN: 239348Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 129278
GnomAD4 exome AF: 0.0000400 AC: 58AN: 1450102Hom.: 0 Cov.: 31 AF XY: 0.0000305 AC XY: 22AN XY: 721132
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152134Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2822G>A (p.R941H) alteration is located in exon 18 (coding exon 18) of the LGR4 gene. This alteration results from a G to A substitution at nucleotide position 2822, causing the arginine (R) at amino acid position 941 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at