chr7-83961734-C-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006080.3(SEMA3A):c.1953G>A(p.Ala651=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00028 in 1,613,790 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00037 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00027 ( 1 hom. )
Consequence
SEMA3A
NM_006080.3 synonymous
NM_006080.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.52
Genes affected
SEMA3A (HGNC:10723): (semaphorin 3A) This gene is a member of the semaphorin family and encodes a protein with an Ig-like C2-type (immunoglobulin-like) domain, a PSI domain and a Sema domain. This secreted protein can function as either a chemorepulsive agent, inhibiting axonal outgrowth, or as a chemoattractive agent, stimulating the growth of apical dendrites. In both cases, the protein is vital for normal neuronal pattern development. Increased expression of this protein is associated with schizophrenia and is seen in a variety of human tumor cell lines. Also, aberrant release of this protein is associated with the progression of Alzheimer's disease. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 7-83961734-C-T is Benign according to our data. Variant chr7-83961734-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 719714.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-3.52 with no splicing effect.
BS2
?
High AC in GnomAd at 57 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3A | NM_006080.3 | c.1953G>A | p.Ala651= | synonymous_variant | 17/17 | ENST00000265362.9 | |
SEMA3A | XM_005250110.4 | c.1953G>A | p.Ala651= | synonymous_variant | 20/20 | ||
SEMA3A | XM_047419751.1 | c.1953G>A | p.Ala651= | synonymous_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3A | ENST00000265362.9 | c.1953G>A | p.Ala651= | synonymous_variant | 17/17 | 1 | NM_006080.3 | P1 | |
SEMA3A | ENST00000436949.5 | c.1953G>A | p.Ala651= | synonymous_variant | 18/18 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000375 AC: 57AN: 152038Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000526 AC: 132AN: 251064Hom.: 0 AF XY: 0.000450 AC XY: 61AN XY: 135680
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GnomAD4 exome AF: 0.000270 AC: 395AN: 1461634Hom.: 1 Cov.: 33 AF XY: 0.000268 AC XY: 195AN XY: 727120
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GnomAD4 genome ? AF: 0.000375 AC: 57AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74372
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 10, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jul 16, 2018 | - - |
SEMA3A-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 11, 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
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Dann
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at