chr3-50159659-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_004186.5(SEMA3F):c.37C>T(p.Leu13=) 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 (★).
Frequency
Genomes: 𝑓 0.054 ( 1579 hom., cov: 33)
Exomes 𝑓: 0.032 ( 10228 hom. )
Consequence
SEMA3F
NM_004186.5 synonymous
NM_004186.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.92
Genes affected
SEMA3F (HGNC:10728): (semaphorin 3F) This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin loop and a C-terminal basic domain. This gene is expressed by the endothelial cells where it was found to act in an autocrine fashion to induce apoptosis, inhibit cell proliferation and survival, and function as an anti-tumorigenic agent. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 3-50159659-C-T is Benign according to our data. Variant chr3-50159659-C-T is described in ClinVar as [Benign]. Clinvar id is 3060222.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=2.92 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3F | NM_004186.5 | c.37C>T | p.Leu13= | synonymous_variant | 2/19 | ENST00000002829.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3F | ENST00000002829.8 | c.37C>T | p.Leu13= | synonymous_variant | 2/19 | 1 | NM_004186.5 |
Frequencies
GnomAD3 genomes AF: 0.0539 AC: 8205AN: 152234Hom.: 1578 Cov.: 33
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GnomAD3 exomes AF: 0.110 AC: 27343AN: 249582Hom.: 6732 AF XY: 0.0906 AC XY: 12252AN XY: 135220
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GnomAD4 exome AF: 0.0325 AC: 47463AN: 1460556Hom.: 10228 Cov.: 29 AF XY: 0.0300 AC XY: 21767AN XY: 726624
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GnomAD4 genome AF: 0.0539 AC: 8212AN: 152352Hom.: 1579 Cov.: 33 AF XY: 0.0623 AC XY: 4645AN XY: 74502
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SEMA3F-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 24, 2022 | 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at