3-50159719-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001318798.2(SEMA3F):c.-108C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000714 in 1,609,690 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 (★).
Frequency
Consequence
NM_001318798.2 5_prime_UTR_premature_start_codon_gain
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: 0.0000657 AC: 10AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000645 AC: 16AN: 248238Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134796
GnomAD4 exome AF: 0.0000720 AC: 105AN: 1457368Hom.: 0 Cov.: 30 AF XY: 0.0000634 AC XY: 46AN XY: 725276
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.97C>T (p.R33W) 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 97, causing the arginine (R) at amino acid position 33 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
SEMA3F-related disorder Uncertain:1
The SEMA3F c.97C>T variant is predicted to result in the amino acid substitution p.Arg33Trp. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.016% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at