5-116447284-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_020796.5(SEMA6A):āc.2422T>Cā(p.Ser808Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000263 in 152,070 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S808F) has been classified as Uncertain significance.
Frequency
Consequence
NM_020796.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6A | NM_020796.5 | c.2422T>C | p.Ser808Pro | missense_variant | 19/19 | ENST00000343348.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6A | ENST00000343348.11 | c.2422T>C | p.Ser808Pro | missense_variant | 19/19 | 1 | NM_020796.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247792Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134718
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 6.84e-7 AC: 1AN: 1461142Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726906
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.2422T>C (p.S808P) alteration is located in exon 19 (coding exon 18) of the SEMA6A gene. This alteration results from a T to C substitution at nucleotide position 2422, causing the serine (S) at amino acid position 808 to be replaced by a proline (P). 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