rs6467991
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000424555.5(SEMA3A):c.-168-18129T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.283 in 151,860 control chromosomes in the GnomAD database, including 8,409 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.28 ( 8409 hom., cov: 31)
Consequence
SEMA3A
ENST00000424555.5 intron
ENST00000424555.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0560
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SEMA3A | ENST00000448879.5 | c.-168-18129T>G | intron_variant | Intron 3 of 4 | 5 | ENSP00000402093.1 | ||||
SEMA3A | ENST00000424555.5 | c.-168-18129T>G | intron_variant | Intron 2 of 3 | 4 | ENSP00000404800.1 | ||||
SEMA3A | ENST00000471474.5 | n.373-18129T>G | intron_variant | Intron 2 of 3 | 5 | |||||
SEMA3A | ENST00000490883.1 | n.152-18129T>G | intron_variant | Intron 2 of 2 | 5 |
Frequencies
GnomAD3 genomes AF: 0.282 AC: 42853AN: 151740Hom.: 8388 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.283 AC: 42924AN: 151860Hom.: 8409 Cov.: 31 AF XY: 0.282 AC XY: 20960AN XY: 74206
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at