7-83961401-G-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_006080.3(SEMA3A):c.2286C>T(p.His762=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,613,976 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 Likely benign (no stars).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
SEMA3A
NM_006080.3 synonymous
NM_006080.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.296
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 7-83961401-G-A is Benign according to our data. Variant chr7-83961401-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3029529.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=0.296 with no splicing effect.
BS2
High AC in GnomAdExome4 at 25 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3A | NM_006080.3 | c.2286C>T | p.His762= | synonymous_variant | 17/17 | ENST00000265362.9 | |
SEMA3A | XM_005250110.4 | c.2286C>T | p.His762= | synonymous_variant | 20/20 | ||
SEMA3A | XM_047419751.1 | c.2286C>T | p.His762= | synonymous_variant | 21/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3A | ENST00000265362.9 | c.2286C>T | p.His762= | synonymous_variant | 17/17 | 1 | NM_006080.3 | P1 | |
SEMA3A | ENST00000436949.5 | c.2286C>T | p.His762= | synonymous_variant | 18/18 | 5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152152Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251398Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135866
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GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461706Hom.: 0 Cov.: 30 AF XY: 0.0000206 AC XY: 15AN XY: 727162
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SEMA3A-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 13, 2023 | 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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