17-44557726-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001466.4(FZD2):c.38C>T(p.Pro13Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000958 in 1,599,778 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P13P) has been classified as Likely benign.
Frequency
Consequence
NM_001466.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00258 AC: 392AN: 151916Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00114 AC: 246AN: 216476Hom.: 0 AF XY: 0.000977 AC XY: 116AN XY: 118732
GnomAD4 exome AF: 0.000787 AC: 1140AN: 1447754Hom.: 3 Cov.: 32 AF XY: 0.000750 AC XY: 540AN XY: 720010
GnomAD4 genome AF: 0.00258 AC: 392AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.00249 AC XY: 185AN XY: 74314
ClinVar
Submissions by phenotype
not provided Benign:2
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FZD2-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at