5-116447034-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_020796.5(SEMA6A):c.2672C>T(p.Pro891Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000361 in 1,613,868 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P891Q) 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 -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA6A | NM_020796.5 | c.2672C>T | p.Pro891Leu | missense_variant | 19/19 | ENST00000343348.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA6A | ENST00000343348.11 | c.2672C>T | p.Pro891Leu | missense_variant | 19/19 | 1 | NM_020796.5 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000342 AC: 52AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000454 AC: 113AN: 249014Hom.: 1 AF XY: 0.000518 AC XY: 70AN XY: 135200
GnomAD4 exome AF: 0.000363 AC: 530AN: 1461694Hom.: 4 Cov.: 31 AF XY: 0.000385 AC XY: 280AN XY: 727126
GnomAD4 genome AF: 0.000342 AC: 52AN: 152174Hom.: 0 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at