chr3-169854938-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_024727.4(LRRC31):c.866T>G(p.Leu289Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000267 in 1,612,748 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 (★).
Frequency
Consequence
NM_024727.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC31 | NM_024727.4 | c.866T>G | p.Leu289Arg | missense_variant | Exon 6 of 9 | ENST00000316428.10 | NP_079003.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC31 | ENST00000316428.10 | c.866T>G | p.Leu289Arg | missense_variant | Exon 6 of 9 | 1 | NM_024727.4 | ENSP00000325978.5 | ||
LRRC31 | ENST00000523069.1 | c.866T>G | p.Leu289Arg | missense_variant | Exon 6 of 9 | 1 | ENSP00000429145.1 | |||
LRRC31 | ENST00000264676.9 | c.698T>G | p.Leu233Arg | missense_variant | Exon 5 of 8 | 2 | ENSP00000264676.5 | |||
LRRC31 | ENST00000397805.2 | n.933T>G | non_coding_transcript_exon_variant | Exon 6 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000184 AC: 28AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000443 AC: 11AN: 248224Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134776
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460478Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726610
GnomAD4 genome AF: 0.000184 AC: 28AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.866T>G (p.L289R) alteration is located in exon 7 (coding exon 6) of the LRRC31 gene. This alteration results from a T to G substitution at nucleotide position 866, causing the leucine (L) at amino acid position 289 to be replaced by an arginine (R). 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