rs1799755
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001164.5(APBB1):c.1965+9_1965+11del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 1,613,122 control chromosomes in the GnomAD database, including 19,806 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.16 ( 2133 hom., cov: 29)
Exomes 𝑓: 0.15 ( 17673 hom. )
Consequence
APBB1
NM_001164.5 intron
NM_001164.5 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.252
Genes affected
APBB1 (HGNC:581): (amyloid beta precursor protein binding family B member 1) The protein encoded by this gene is a member of the Fe65 protein family. It is an adaptor protein localized in the nucleus. It interacts with the Alzheimer's disease amyloid precursor protein (APP), transcription factor CP2/LSF/LBP1 and the low-density lipoprotein receptor-related protein. APP functions as a cytosolic anchoring site that can prevent the gene product's nuclear translocation. This encoded protein could play an important role in the pathogenesis of Alzheimer's disease. It is thought to regulate transcription. Also it is observed to block cell cycle progression by downregulating thymidylate synthase expression. Multiple alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
APBB1 | NM_001164.5 | c.1965+9_1965+11del | intron_variant | ENST00000609360.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
APBB1 | ENST00000609360.6 | c.1965+9_1965+11del | intron_variant | 5 | NM_001164.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.161 AC: 24403AN: 151962Hom.: 2124 Cov.: 29
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GnomAD3 exomes AF: 0.150 AC: 37393AN: 249784Hom.: 3325 AF XY: 0.154 AC XY: 20798AN XY: 134990
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GnomAD4 exome AF: 0.149 AC: 217161AN: 1461042Hom.: 17673 AF XY: 0.152 AC XY: 110429AN XY: 726802
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GnomAD4 genome ? AF: 0.161 AC: 24438AN: 152080Hom.: 2133 Cov.: 29 AF XY: 0.161 AC XY: 11963AN XY: 74346
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at