chr7-83367330-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_012431.3(SEMA3E):c.*256T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0274 in 406,682 control chromosomes in the GnomAD database, including 1,088 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.061 ( 929 hom., cov: 32)
Exomes 𝑓: 0.0075 ( 159 hom. )
Consequence
SEMA3E
NM_012431.3 3_prime_UTR
NM_012431.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0480
Genes affected
SEMA3E (HGNC:10727): (semaphorin 3E) Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]
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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=-0.85).
BP6
?
Variant 7-83367330-A-G is Benign according to our data. Variant chr7-83367330-A-G is described in ClinVar as [Benign]. Clinvar id is 1242507.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3E | NM_012431.3 | c.*256T>C | 3_prime_UTR_variant | 17/17 | ENST00000643230.2 | ||
SEMA3E | NM_001178129.2 | c.*256T>C | 3_prime_UTR_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3E | ENST00000643230.2 | c.*256T>C | 3_prime_UTR_variant | 17/17 | NM_012431.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0604 AC: 9186AN: 152134Hom.: 928 Cov.: 32
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GnomAD4 exome AF: 0.00750 AC: 1909AN: 254430Hom.: 159 Cov.: 3 AF XY: 0.00630 AC XY: 843AN XY: 133914
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GnomAD4 genome ? AF: 0.0605 AC: 9217AN: 152252Hom.: 929 Cov.: 32 AF XY: 0.0580 AC XY: 4320AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 22, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at