GeneBe

rs56314229

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_017439.4(GSAP):​c.577-23_577-11delTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000092 in 1,086,470 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 9.2e-7 ( 0 hom. )

Consequence

GSAP
NM_017439.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.21

Publications

0 publications found
Variant links:
Genes affected
GSAP (HGNC:28042): (gamma-secretase activating protein) Accumulation of neurotoxic amyloid-beta is a major hallmark of Alzheimer disease (AD; MIM 104300). Formation of amyloid-beta is catalyzed by gamma-secretase (see PSEN1; MIM 104311), a protease with numerous substrates. PION, or GSAP, selectively increases amyloid-beta production through a mechanism involving its interaction with both gamma-secretase and its substrate, the amyloid-beta precursor protein (APP; MIM 104760) C-terminal fragment (APP-CTF) (He et al., 2010 [PubMed 20811458]).[supplied by OMIM, Nov 2010]

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GSAPNM_017439.4 linkc.577-23_577-11delTTTTTTTTTTTTT intron_variant Intron 8 of 30 ENST00000257626.12 NP_059135.2 A4D1B5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GSAPENST00000257626.12 linkc.577-23_577-11delTTTTTTTTTTTTT intron_variant Intron 8 of 30 1 NM_017439.4 ENSP00000257626.7 A4D1B5-1
GSAPENST00000334003.11 linkn.468-23_468-11delTTTTTTTTTTTTT intron_variant Intron 7 of 18 2

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
9.20e-7
AC:
1
AN:
1086470
Hom.:
0
AF XY:
0.00000187
AC XY:
1
AN XY:
534570
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
22962
American (AMR)
AF:
0.00
AC:
0
AN:
20908
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
14920
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24036
South Asian (SAS)
AF:
0.00
AC:
0
AN:
52472
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
24172
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
3056
European-Non Finnish (NFE)
AF:
0.00000113
AC:
1
AN:
881266
Other (OTH)
AF:
0.00
AC:
0
AN:
42678
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
2.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs56314229; hg19: chr7-77006717; API