chr1-84865715-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_012152.3(LPAR3):c.406G>T(p.Val136Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,158 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_012152.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LPAR3 | ENST00000370611.4 | c.406G>T | p.Val136Phe | missense_variant | Exon 2 of 3 | 1 | NM_012152.3 | ENSP00000359643.3 | ||
LPAR3 | ENST00000440886.1 | c.406G>T | p.Val136Phe | missense_variant | Exon 1 of 2 | 1 | ENSP00000395389.1 | |||
LPAR3 | ENST00000491034.1 | n.430G>T | non_coding_transcript_exon_variant | Exon 1 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251316Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135838
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727246
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.406G>T (p.V136F) alteration is located in exon 2 (coding exon 1) of the LPAR3 gene. This alteration results from a G to T substitution at nucleotide position 406, causing the valine (V) at amino acid position 136 to be replaced by a phenylalanine (F). 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