rs7780132
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001384900.1(SEMA3D):c.1545+91G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 794,442 control chromosomes in the GnomAD database, including 120,812 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 0.58 ( 26333 hom., cov: 32)
Exomes 𝑓: 0.54 ( 94479 hom. )
Consequence
SEMA3D
NM_001384900.1 intron
NM_001384900.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.50
Genes affected
SEMA3D (HGNC:10726): (semaphorin 3D) This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]
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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=-0.87).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3D | NM_001384900.1 | c.1545+91G>A | intron_variant | ENST00000284136.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3D | ENST00000284136.11 | c.1545+91G>A | intron_variant | 5 | NM_001384900.1 | P1 | |||
SEMA3D | ENST00000484038.1 | n.671+91G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.580 AC: 87788AN: 151308Hom.: 26278 Cov.: 32
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GnomAD4 exome AF: 0.537 AC: 345046AN: 643016Hom.: 94479 AF XY: 0.535 AC XY: 183965AN XY: 343722
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GnomAD4 genome ? AF: 0.581 AC: 87905AN: 151426Hom.: 26333 Cov.: 32 AF XY: 0.574 AC XY: 42437AN XY: 73960
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at