11-27368556-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBS2_Supporting
The NM_018490.5(LGR4):c.2167G>A(p.Val723Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000335 in 1,613,322 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 (★). Synonymous variant affecting the same amino acid position (i.e. V723V) has been classified as Likely benign.
Frequency
Consequence
NM_018490.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGR4 | ENST00000379214.9 | c.2167G>A | p.Val723Ile | missense_variant | Exon 18 of 18 | 1 | NM_018490.5 | ENSP00000368516.4 | ||
LGR4 | ENST00000389858.4 | c.2095G>A | p.Val699Ile | missense_variant | Exon 17 of 17 | 1 | ENSP00000374508.4 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251114Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135738
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461272Hom.: 0 Cov.: 34 AF XY: 0.0000358 AC XY: 26AN XY: 726978
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74266
ClinVar
Submissions by phenotype
not specified Benign:1
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