rs3735514
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006080.3(SEMA3A):c.1361-155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,082 control chromosomes in the GnomAD database, including 4,306 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.23 ( 4306 hom., cov: 33)
Consequence
SEMA3A
NM_006080.3 intron
NM_006080.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0760
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 7-84002201-T-C is Benign according to our data. Variant chr7-84002201-T-C is described in ClinVar as [Benign]. Clinvar id is 1234621.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| SEMA3A | NM_006080.3 | c.1361-155A>G | intron_variant | Intron 11 of 16 | ENST00000265362.9 | NP_006071.1 | ||
| SEMA3A | XM_005250110.4 | c.1361-155A>G | intron_variant | Intron 14 of 19 | XP_005250167.1 | |||
| SEMA3A | XM_047419751.1 | c.1361-155A>G | intron_variant | Intron 15 of 20 | XP_047275707.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.235 AC: 35661AN: 151964Hom.: 4307 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome 0.235 AC: 35670AN: 152082Hom.: 4306 Cov.: 33 AF XY: 0.238 AC XY: 17726AN XY: 74346
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3476
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Aug 09, 2018
GeneDx
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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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