chr11-57182465-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001005210.4(LRRC55):c.443C>T(p.Pro148Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000559 in 1,610,854 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_001005210.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRRC55 | NM_001005210.4 | c.443C>T | p.Pro148Leu | missense_variant | Exon 1 of 2 | ENST00000497933.3 | NP_001005210.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LRRC55 | ENST00000497933.3 | c.443C>T | p.Pro148Leu | missense_variant | Exon 1 of 2 | 1 | NM_001005210.4 | ENSP00000419542.2 | ||
LRRC55 | ENST00000652194.1 | c.572C>T | p.Pro191Leu | missense_variant | Exon 1 of 2 | ENSP00000498533.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249022Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134762
GnomAD4 exome AF: 0.0000555 AC: 81AN: 1458618Hom.: 0 Cov.: 32 AF XY: 0.0000524 AC XY: 38AN XY: 725458
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.572C>T (p.P191L) alteration is located in exon 1 (coding exon 1) of the LRRC55 gene. This alteration results from a C to T substitution at nucleotide position 572, causing the proline (P) at amino acid position 191 to be replaced by a leucine (L). 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