chr21-25881080-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000484.4(APP):c.*590C>A variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.00841 in 156,406 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000484.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APP | NM_000484.4 | c.*590C>A | 3_prime_UTR_variant | Exon 18 of 18 | ENST00000346798.8 | NP_000475.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00857 AC: 1304AN: 152142Hom.: 20 Cov.: 32
GnomAD4 exome AF: 0.000241 AC: 1AN: 4146Hom.: 0 Cov.: 0 AF XY: 0.000444 AC XY: 1AN XY: 2252
GnomAD4 genome AF: 0.00864 AC: 1315AN: 152260Hom.: 21 Cov.: 32 AF XY: 0.00854 AC XY: 636AN XY: 74438
ClinVar
Submissions by phenotype
Alzheimer disease Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at