chr12-62525185-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_015026.3(MON2):c.1211C>T(p.Pro404Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000198 in 1,613,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P404S) has been classified as Uncertain significance.
Frequency
Consequence
NM_015026.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152030Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251090Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135730
GnomAD4 exome AF: 0.000206 AC: 301AN: 1461088Hom.: 0 Cov.: 31 AF XY: 0.000215 AC XY: 156AN XY: 726892
GnomAD4 genome AF: 0.000125 AC: 19AN: 152030Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1211C>T (p.P404L) alteration is located in exon 10 (coding exon 10) of the MON2 gene. This alteration results from a C to T substitution at nucleotide position 1211, causing the proline (P) at amino acid position 404 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