rs10487865
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Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1
The NM_006080.3(SEMA3A):āc.1563G>Cā(p.Gly521=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0296 in 1,613,724 control chromosomes in the GnomAD database, including 2,323 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.026 ( 165 hom., cov: 32)
Exomes š: 0.030 ( 2158 hom. )
Consequence
SEMA3A
NM_006080.3 synonymous
NM_006080.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.202
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 -19 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.35).
BP6
?
Variant 7-83981410-C-G is Benign according to our data. Variant chr7-83981410-C-G is described in ClinVar as [Benign]. Clinvar id is 1262671.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-83981410-C-G is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=-0.202 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3A | NM_006080.3 | c.1563G>C | p.Gly521= | synonymous_variant | 14/17 | ENST00000265362.9 | |
SEMA3A | XM_005250110.4 | c.1563G>C | p.Gly521= | synonymous_variant | 17/20 | ||
SEMA3A | XM_047419751.1 | c.1563G>C | p.Gly521= | synonymous_variant | 18/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3A | ENST00000265362.9 | c.1563G>C | p.Gly521= | synonymous_variant | 14/17 | 1 | NM_006080.3 | P1 | |
SEMA3A | ENST00000436949.5 | c.1563G>C | p.Gly521= | synonymous_variant | 15/18 | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0259 AC: 3932AN: 152086Hom.: 165 Cov.: 32
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GnomAD3 exomes AF: 0.0505 AC: 12670AN: 250762Hom.: 750 AF XY: 0.0500 AC XY: 6773AN XY: 135572
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GnomAD4 exome AF: 0.0300 AC: 43847AN: 1461520Hom.: 2158 Cov.: 31 AF XY: 0.0318 AC XY: 23122AN XY: 727056
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GnomAD4 genome ? AF: 0.0259 AC: 3935AN: 152204Hom.: 165 Cov.: 32 AF XY: 0.0284 AC XY: 2115AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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