11-117291048-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_012104.6(BACE1):c.944C>T(p.Thr315Met) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,918 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012104.6 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BACE1 | NM_012104.6 | c.944C>T | p.Thr315Met | missense_variant, splice_region_variant | Exon 7 of 9 | ENST00000313005.11 | NP_036236.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251156Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135730
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461698Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727130
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.944C>T (p.T315M) alteration is located in exon 7 (coding exon 7) of the BACE1 gene. This alteration results from a C to T substitution at nucleotide position 944, causing the threonine (T) at amino acid position 315 to be replaced by a methionine (M). 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