rs649483
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4BA1
The ENST00000558014.5(SEMA6D):c.-238-62691A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.467 in 152,090 control chromosomes in the GnomAD database, including 19,714 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 0.47 ( 19714 hom., cov: 33)
Consequence
SEMA6D
ENST00000558014.5 intron
ENST00000558014.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.73
Genes affected
SEMA6D (HGNC:16770): (semaphorin 6D) Semaphorins are a large family, including both secreted and membrane associated proteins, many of which have been implicated as inhibitors or chemorepellents in axon pathfinding, fasciculation and branching, and target selection. All semaphorins possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Additional sequence motifs C-terminal to the semaphorin domain allow classification into distinct subfamilies. Results demonstrate that transmembrane semaphorins, like the secreted ones, can act as repulsive axon guidance cues. This gene encodes a class 6 vertebrate transmembrane semaphorin that demonstrates alternative splicing. Several transcript variants have been identified and expression of the distinct encoded isoforms is thought to be regulated in a tissue- and development-dependent manner. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.17).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6D | NM_001198999.2 | c.-238-62691A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6D | ENST00000558014.5 | c.-238-62691A>G | intron_variant | 1 | A1 | ||||
SEMA6D | ENST00000559184.5 | c.-238-62691A>G | intron_variant | 4 | |||||
SEMA6D | ENST00000560636.5 | c.-323+10483A>G | intron_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.468 AC: 71064AN: 151972Hom.: 19731 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.467 AC: 71040AN: 152090Hom.: 19714 Cov.: 33 AF XY: 0.475 AC XY: 35338AN XY: 74346
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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