rs442173
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003966.3(SEMA5A):c.-175+36678C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,218 control chromosomes in the GnomAD database, including 62,170 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 0.90 ( 62170 hom., cov: 32)
Consequence
SEMA5A
NM_003966.3 intron
NM_003966.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.04
Genes affected
SEMA5A (HGNC:10736): (semaphorin 5A) This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]
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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=-1.0).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA5A | NM_003966.3 | c.-175+36678C>T | intron_variant | ENST00000382496.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA5A | ENST00000382496.10 | c.-175+36678C>T | intron_variant | 1 | NM_003966.3 | P1 | |||
SEMA5A | ENST00000652226.1 | c.-393+36678C>T | intron_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.903 AC: 137300AN: 152100Hom.: 62142 Cov.: 32
GnomAD3 genomes
?
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152100
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.903 AC: 137380AN: 152218Hom.: 62170 Cov.: 32 AF XY: 0.899 AC XY: 66884AN XY: 74412
GnomAD4 genome
?
AF:
AC:
137380
AN:
152218
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32
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66884
AN XY:
74412
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Asia WGS
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2544
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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