chr10-48914014-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001378102.1(LRRC18):c.142C>T(p.Arg48Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000954 in 1,614,054 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/21 in silico tools predict a benign 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. R48S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001378102.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LRRC18 | NM_001378102.1 | c.142C>T | p.Arg48Cys | missense_variant | 3/4 | ENST00000374160.8 | |
WDFY4 | NM_001394531.1 | c.7586+12151G>A | intron_variant | ENST00000325239.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LRRC18 | ENST00000374160.8 | c.142C>T | p.Arg48Cys | missense_variant | 3/4 | 1 | NM_001378102.1 | P1 | |
WDFY4 | ENST00000325239.12 | c.7586+12151G>A | intron_variant | 5 | NM_001394531.1 | P1 | |||
ENST00000430438.1 | n.173+18472C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000107 AC: 27AN: 251442Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135906
GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461884Hom.: 0 Cov.: 60 AF XY: 0.0000880 AC XY: 64AN XY: 727242
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2023 | The c.142C>T (p.R48C) alteration is located in exon 1 (coding exon 1) of the LRRC18 gene. This alteration results from a C to T substitution at nucleotide position 142, causing the arginine (R) at amino acid position 48 to be replaced by a cysteine (C). 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