NM_001365715.1:c.199C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001365715.1(LRCH3):c.199C>T(p.Arg67Trp) variant causes a missense change. The variant allele was found at a frequency of 0.000273 in 1,601,298 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365715.1 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LRCH3 | NM_001365715.1 | c.199C>T | p.Arg67Trp | missense_variant | Exon 1 of 21 | ENST00000425562.7 | NP_001352644.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152146Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000173 AC: 39AN: 224966Hom.: 1 AF XY: 0.000234 AC XY: 29AN XY: 123708
GnomAD4 exome AF: 0.000283 AC: 410AN: 1449152Hom.: 1 Cov.: 32 AF XY: 0.000285 AC XY: 205AN XY: 720400
GnomAD4 genome AF: 0.000177 AC: 27AN: 152146Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.199C>T (p.R67W) alteration is located in exon 1 (coding exon 1) of the LRCH3 gene. This alteration results from a C to T substitution at nucleotide position 199, causing the arginine (R) at amino acid position 67 to be replaced by a tryptophan (W). 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