11-27368148-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4BS2_Supporting
The NM_018490.5(LGR4):c.2575G>A(p.Asp859Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D859H) has been classified as Uncertain significance.
Frequency
Consequence
NM_018490.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LGR4 | ENST00000379214.9 | c.2575G>A | p.Asp859Asn | missense_variant | Exon 18 of 18 | 1 | NM_018490.5 | ENSP00000368516.4 | ||
LGR4 | ENST00000389858.4 | c.2503G>A | p.Asp835Asn | missense_variant | Exon 17 of 17 | 1 | ENSP00000374508.4 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251420Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135882
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461850Hom.: 0 Cov.: 38 AF XY: 0.00000688 AC XY: 5AN XY: 727228
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2575G>A (p.D859N) 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 2575, causing the aspartic acid (D) at amino acid position 859 to be replaced by an asparagine (N). 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