rs1057077
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001135217.2(LRRC23):c.950T>A(p.Val317Glu) variant causes a missense change. The variant allele was found at a frequency of 0.298 in 1,613,650 control chromosomes in the GnomAD database, including 77,324 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001135217.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC23 | NM_001135217.2 | c.950T>A | p.Val317Glu | missense_variant | 7/8 | ENST00000443597.7 | |
LRRC23 | NM_201650.3 | c.950T>A | p.Val317Glu | missense_variant | 7/8 | ||
LRRC23 | NM_006992.4 | c.759-970T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC23 | ENST00000443597.7 | c.950T>A | p.Val317Glu | missense_variant | 7/8 | 1 | NM_001135217.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.375 AC: 56942AN: 151692Hom.: 12430 Cov.: 31
GnomAD3 exomes AF: 0.297 AC: 74574AN: 251474Hom.: 12452 AF XY: 0.297 AC XY: 40407AN XY: 135914
GnomAD4 exome AF: 0.290 AC: 424413AN: 1461840Hom.: 64872 Cov.: 38 AF XY: 0.292 AC XY: 212169AN XY: 727226
GnomAD4 genome ? AF: 0.376 AC: 57011AN: 151810Hom.: 12452 Cov.: 31 AF XY: 0.370 AC XY: 27483AN XY: 74194
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at