11-117293131-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_012104.6(BACE1):c.763C>T(p.Arg255Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000285 in 1,614,028 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R255Q) has been classified 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 -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BACE1 | NM_012104.6 | c.763C>T | p.Arg255Trp | missense_variant | 5/9 | ENST00000313005.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BACE1 | ENST00000313005.11 | c.763C>T | p.Arg255Trp | missense_variant | 5/9 | 1 | NM_012104.6 | P1 | |
BACE1-AS | ENST00000614401.1 | n.305G>A | non_coding_transcript_exon_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152076Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251342Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135838
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461834Hom.: 0 Cov.: 33 AF XY: 0.0000220 AC XY: 16AN XY: 727216
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152194Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74408
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.763C>T (p.R255W) alteration is located in exon 5 (coding exon 5) of the BACE1 gene. This alteration results from a C to T substitution at nucleotide position 763, causing the arginine (R) at amino acid position 255 to be replaced by a tryptophan (W). 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