chr3-122913200-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001031702.4(SEMA5B):c.2505C>A(p.Asp835Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000071 in 1,408,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/23 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031702.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA5B | NM_001031702.4 | c.2505C>A | p.Asp835Glu | missense_variant, splice_region_variant | 17/23 | ENST00000357599.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA5B | ENST00000357599.8 | c.2505C>A | p.Asp835Glu | missense_variant, splice_region_variant | 17/23 | 1 | NM_001031702.4 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 7.10e-7 AC: 1AN: 1408980Hom.: 0 Cov.: 33 AF XY: 0.00000143 AC XY: 1AN XY: 698366
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.2505C>A (p.D835E) alteration is located in exon 17 (coding exon 16) of the SEMA5B gene. This alteration results from a C to A substitution at nucleotide position 2505, causing the aspartic acid (D) at amino acid position 835 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.