3-50159626-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004186.5(SEMA3F):c.4C>T(p.Leu2Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000413 in 1,452,356 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L2V) has been classified as Uncertain significance.
Frequency
Consequence
NM_004186.5 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 Cov.: 33
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 246224Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133552
GnomAD4 exome AF: 0.00000413 AC: 6AN: 1452356Hom.: 0 Cov.: 28 AF XY: 0.00000415 AC XY: 3AN XY: 723078
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.4C>T (p.L2F) alteration is located in exon 2 (coding exon 1) of the SEMA3F gene. This alteration results from a C to T substitution at nucleotide position 4, causing the leucine (L) at amino acid position 2 to be replaced by a phenylalanine (F). 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