5-116446915-C-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_020796.5(SEMA6A):āc.2791G>Cā(p.Ala931Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00334 in 1,613,964 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A931T) has been classified as Uncertain significance.
Frequency
Consequence
NM_020796.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6A | NM_020796.5 | c.2791G>C | p.Ala931Pro | missense_variant | 19/19 | ENST00000343348.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6A | ENST00000343348.11 | c.2791G>C | p.Ala931Pro | missense_variant | 19/19 | 1 | NM_020796.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00221 AC: 336AN: 152134Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00190 AC: 474AN: 249254Hom.: 3 AF XY: 0.00173 AC XY: 234AN XY: 135220
GnomAD4 exome AF: 0.00346 AC: 5058AN: 1461712Hom.: 7 Cov.: 31 AF XY: 0.00338 AC XY: 2458AN XY: 727138
GnomAD4 genome AF: 0.00221 AC: 336AN: 152252Hom.: 1 Cov.: 32 AF XY: 0.00173 AC XY: 129AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at