1-152776433-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_178354.3(LCE1F):c.62C>T(p.Pro21Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000086 in 1,603,944 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000281 AC: 40AN: 142310Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251416Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135884
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1461534Hom.: 0 Cov.: 31 AF XY: 0.0000646 AC XY: 47AN XY: 727082
GnomAD4 genome AF: 0.000281 AC: 40AN: 142410Hom.: 0 Cov.: 31 AF XY: 0.000245 AC XY: 17AN XY: 69458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.62C>T (p.P21L) 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 62, causing the proline (P) at amino acid position 21 to be replaced by a leucine (L). 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