chr3-50159677-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004186.5(SEMA3F):āc.55T>Cā(p.Ser19Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000142 in 1,613,256 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S19F) has been classified as Uncertain significance.
Frequency
Consequence
NM_004186.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3F | NM_004186.5 | c.55T>C | p.Ser19Pro | missense_variant | 2/19 | ENST00000002829.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3F | ENST00000002829.8 | c.55T>C | p.Ser19Pro | missense_variant | 2/19 | 1 | NM_004186.5 |
Frequencies
GnomAD3 genomes ? AF: 0.000802 AC: 122AN: 152206Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000164 AC: 41AN: 249868Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135342
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1460932Hom.: 1 Cov.: 31 AF XY: 0.0000509 AC XY: 37AN XY: 726784
GnomAD4 genome ? AF: 0.000801 AC: 122AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74486
ClinVar
Submissions by phenotype
SEMA3F-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 15, 2022 | This variant is classified as likely 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