chr9-128151921-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005564.5(LCN2):c.371C>T(p.Thr124Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,614,110 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005564.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00761 AC: 1159AN: 152202Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.00212 AC: 534AN: 251394Hom.: 7 AF XY: 0.00160 AC XY: 217AN XY: 135864
GnomAD4 exome AF: 0.000757 AC: 1107AN: 1461790Hom.: 17 Cov.: 36 AF XY: 0.000656 AC XY: 477AN XY: 727198
GnomAD4 genome AF: 0.00766 AC: 1167AN: 152320Hom.: 15 Cov.: 33 AF XY: 0.00737 AC XY: 549AN XY: 74486
ClinVar
Submissions by phenotype
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at