chr16-69954392-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001370523.4(CLEC18A):c.275C>T(p.Pro92Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 150,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370523.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLEC18A | NM_001370523.4 | c.275C>T | p.Pro92Leu | missense_variant | Exon 3 of 12 | ENST00000288040.11 | NP_001357452.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000533 AC: 8AN: 150066Hom.: 0 Cov.: 26
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248526Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134520
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000117 AC: 171AN: 1459756Hom.: 0 Cov.: 71 AF XY: 0.000121 AC XY: 88AN XY: 726244
GnomAD4 genome AF: 0.0000533 AC: 8AN: 150066Hom.: 0 Cov.: 26 AF XY: 0.0000274 AC XY: 2AN XY: 73094
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.275C>T (p.P92L) alteration is located in exon 4 (coding exon 3) of the CLEC18A gene. This alteration results from a C to T substitution at nucleotide position 275, causing the proline (P) at amino acid position 92 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