NM_013437.5:c.2168G>A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_013437.5(LRP12):c.2168G>A(p.Arg723His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000638 in 1,614,120 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R723C) has been classified as Uncertain significance.
Frequency
Consequence
NM_013437.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRP12 | ENST00000276654.10 | c.2168G>A | p.Arg723His | missense_variant | Exon 7 of 7 | 1 | NM_013437.5 | ENSP00000276654.5 | ||
LRP12 | ENST00000424843.6 | c.2111G>A | p.Arg704His | missense_variant | Exon 6 of 6 | 2 | ENSP00000399148.2 | |||
LRP12 | ENST00000518375.1 | n.1521G>A | non_coding_transcript_exon_variant | Exon 2 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000995 AC: 25AN: 251164Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135746
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461870Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 727238
GnomAD4 genome AF: 0.000105 AC: 16AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000941 AC XY: 7AN XY: 74420
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.2168G>A (p.R723H) alteration is located in exon 7 (coding exon 7) of the LRP12 gene. This alteration results from a G to A substitution at nucleotide position 2168, causing the arginine (R) at amino acid position 723 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