11-117289613-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_012104.6(BACE1):c.1459C>T(p.Arg487Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000663 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012104.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BACE1 | NM_012104.6 | c.1459C>T | p.Arg487Cys | missense_variant | Exon 9 of 9 | ENST00000313005.11 | NP_036236.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250678Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135580
GnomAD4 exome AF: 0.0000657 AC: 96AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.0000715 AC XY: 52AN XY: 727242
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1459C>T (p.R487C) alteration is located in exon 9 (coding exon 9) of the BACE1 gene. This alteration results from a C to T substitution at nucleotide position 1459, causing the arginine (R) at amino acid position 487 to be replaced by a cysteine (C). 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