1-152805247-T-G
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178351.4(LCE1C):c.232A>C(p.Ser78Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,613,804 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 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
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000855 AC: 13AN: 152034Hom.: 0 Cov.: 31 show subpopulations
GnomAD2 exomes AF: 0.0000919 AC: 23AN: 250136 AF XY: 0.0000812 show subpopulations
GnomAD4 exome AF: 0.0000705 AC: 103AN: 1461652Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 49AN XY: 727130 show subpopulations
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152152Hom.: 0 Cov.: 31 AF XY: 0.0000941 AC XY: 7AN XY: 74376 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.232A>C (p.S78R) alteration is located in exon 2 (coding exon 1) of the LCE1C gene. This alteration results from a A to C substitution at nucleotide position 232, causing the serine (S) at amino acid position 78 to be replaced by an arginine (R). 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