3-50159659-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_004186.5(SEMA3F):c.37C>T(p.Leu13Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0345 in 1,612,908 control chromosomes in the GnomAD database, including 11,807 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_004186.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0539 AC: 8205AN: 152234Hom.: 1578 Cov.: 33
GnomAD3 exomes AF: 0.110 AC: 27343AN: 249582Hom.: 6732 AF XY: 0.0906 AC XY: 12252AN XY: 135220
GnomAD4 exome AF: 0.0325 AC: 47463AN: 1460556Hom.: 10228 Cov.: 29 AF XY: 0.0300 AC XY: 21767AN XY: 726624
GnomAD4 genome AF: 0.0539 AC: 8212AN: 152352Hom.: 1579 Cov.: 33 AF XY: 0.0623 AC XY: 4645AN XY: 74502
ClinVar
Submissions by phenotype
SEMA3F-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