chr9-136953919-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_178536.4(LCN12):c.403C>T(p.Arg135Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,611,498 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_178536.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LCN12 | NM_178536.4 | c.403C>T | p.Arg135Cys | missense_variant | Exon 4 of 6 | ENST00000371633.8 | NP_848631.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000245 AC: 6AN: 244400Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133484
GnomAD4 exome AF: 0.00000754 AC: 11AN: 1459332Hom.: 0 Cov.: 52 AF XY: 0.00000275 AC XY: 2AN XY: 726032
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.403C>T (p.R135C) alteration is located in exon 4 (coding exon 4) of the LCN12 gene. This alteration results from a C to T substitution at nucleotide position 403, causing the arginine (R) at amino acid position 135 to be replaced by a cysteine (C). 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