19-4543910-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032108.4(SEMA6B):c.2358C>A(p.Asp786Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000407 in 1,203,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032108.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6B | NM_032108.4 | c.2358C>A | p.Asp786Glu | missense_variant | 17/17 | ENST00000586582.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6B | ENST00000586582.6 | c.2358C>A | p.Asp786Glu | missense_variant | 17/17 | 1 | NM_032108.4 | P1 | |
SEMA6B | ENST00000586965.1 | c.1851+507C>A | intron_variant | 1 | |||||
SEMA6B | ENST00000676793.1 | c.2358C>A | p.Asp786Glu | missense_variant | 17/17 | P1 | |||
SEMA6B | ENST00000677828.1 | c.*1620C>A | 3_prime_UTR_variant, NMD_transcript_variant | 17/17 |
Frequencies
GnomAD3 genomes ? AF: 0.0000529 AC: 8AN: 151174Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000390 AC: 41AN: 1051742Hom.: 0 Cov.: 33 AF XY: 0.0000423 AC XY: 21AN XY: 496324
GnomAD4 genome ? AF: 0.0000529 AC: 8AN: 151280Hom.: 0 Cov.: 32 AF XY: 0.0000676 AC XY: 5AN XY: 73924
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 01, 2021 | The c.2358C>A (p.D786E) alteration is located in exon 17 (coding exon 16) of the SEMA6B gene. This alteration results from a C to A substitution at nucleotide position 2358, causing the aspartic acid (D) at amino acid position 786 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