NM_001395660.1:c.689G>A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001395660.1(LPAR2):c.689G>A(p.Arg230Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,612,624 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_001395660.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LPAR2 | NM_001395660.1 | c.689G>A | p.Arg230Gln | missense_variant | Exon 2 of 3 | ENST00000407877.8 | NP_001382589.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LPAR2 | ENST00000407877.8 | c.689G>A | p.Arg230Gln | missense_variant | Exon 2 of 3 | 1 | NM_001395660.1 | ENSP00000384665.3 | ||
LPAR2 | ENST00000542587.5 | c.689G>A | p.Arg230Gln | missense_variant | Exon 5 of 6 | 2 | ENSP00000443256.2 | |||
LPAR2 | ENST00000586703.1 | c.689G>A | p.Arg230Gln | missense_variant | Exon 2 of 3 | 1 | ENSP00000465280.2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152212Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248128Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134850
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1460294Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726480
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152330Hom.: 0 Cov.: 31 AF XY: 0.0000805 AC XY: 6AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.698G>A (p.R233Q) alteration is located in exon 2 (coding exon 1) of the LPAR2 gene. This alteration results from a G to A substitution at nucleotide position 698, causing the arginine (R) at amino acid position 233 to be replaced by a glutamine (Q). 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