chr1-152805174-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_178351.4(LCE1C):c.305G>T(p.Gly102Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000548 in 1,460,460 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178351.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCE1C | NM_178351.4 | c.305G>T | p.Gly102Val | missense_variant | 2/2 | ENST00000607093.2 | |
LCE1C | NM_001276331.2 | c.215G>T | p.Gly72Val | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCE1C | ENST00000607093.2 | c.305G>T | p.Gly102Val | missense_variant | 2/2 | NM_178351.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 152100Hom.: 0 Cov.: 31 FAILED QC
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 248166Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134796
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460460Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726446
GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 152100Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.305G>T (p.G102V) alteration is located in exon 2 (coding exon 1) of the LCE1C gene. This alteration results from a G to T substitution at nucleotide position 305, causing the glycine (G) at amino acid position 102 to be replaced by a valine (V). 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