chr1-152776486-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178354.3(LCE1F):c.115C>T(p.Pro39Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000999 in 1,601,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178354.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000566 AC: 8AN: 141236Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251396Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135880
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1459756Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726162
GnomAD4 genome AF: 0.0000566 AC: 8AN: 141340Hom.: 0 Cov.: 32 AF XY: 0.0000436 AC XY: 3AN XY: 68884
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.115C>T (p.P39S) alteration is located in exon 1 (coding exon 1) of the LCE1F gene. This alteration results from a C to T substitution at nucleotide position 115, causing the proline (P) at amino acid position 39 to be replaced by a serine (S). 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