chr8-85109747-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_033402.5(LRRCC1):āc.257T>Cā(p.Leu86Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,599,898 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L86V) has been classified as Uncertain significance.
Frequency
Consequence
NM_033402.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRCC1 | NM_033402.5 | c.257T>C | p.Leu86Pro | missense_variant | 2/19 | ENST00000360375.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRCC1 | ENST00000360375.8 | c.257T>C | p.Leu86Pro | missense_variant | 2/19 | 1 | NM_033402.5 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244346Hom.: 0 AF XY: 0.00000755 AC XY: 1AN XY: 132510
GnomAD4 exome AF: 0.00000898 AC: 13AN: 1447702Hom.: 0 Cov.: 27 AF XY: 0.00000972 AC XY: 7AN XY: 720426
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 07, 2024 | The c.257T>C (p.L86P) alteration is located in exon 2 (coding exon 2) of the LRRCC1 gene. This alteration results from a T to C substitution at nucleotide position 257, causing the leucine (L) at amino acid position 86 to be replaced by a proline (P). 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