chr1-84865874-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM2PP3_ModerateBS2
The NM_012152.3(LPAR3):c.247T>A(p.Tyr83Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. Y83C) has been classified as Uncertain significance.
Frequency
Consequence
NM_012152.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LPAR3 | NM_012152.3 | c.247T>A | p.Tyr83Asn | missense_variant | 2/3 | ENST00000370611.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LPAR3 | ENST00000370611.4 | c.247T>A | p.Tyr83Asn | missense_variant | 2/3 | 1 | NM_012152.3 | P1 | |
LPAR3 | ENST00000440886.1 | c.247T>A | p.Tyr83Asn | missense_variant | 1/2 | 1 | P1 | ||
LPAR3 | ENST00000491034.1 | n.271T>A | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251228Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135784
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727246
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.247T>A (p.Y83N) alteration is located in exon 2 (coding exon 1) of the LPAR3 gene. This alteration results from a T to A substitution at nucleotide position 247, causing the tyrosine (Y) at amino acid position 83 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