NM_017439.4:c.577-14_577-11dupTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_017439.4(GSAP):​c.577-14_577-11dupTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000097 ( 0 hom. )

Consequence

GSAP
NM_017439.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GSAPNM_017439.4 linkc.577-14_577-11dupTTTT 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.577-11_577-10insTTTT intron_variant Intron 8 of 30 1 NM_017439.4 ENSP00000257626.7 A4D1B5-1
GSAPENST00000334003.11 linkn.468-11_468-10insTTTT intron_variant Intron 7 of 18 2

Frequencies

GnomAD3 genomes
AF:
0.000133
AC:
13
AN:
98068
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000121
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000316
Gnomad SAS
AF:
0.000339
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000783
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000967
AC:
105
AN:
1086372
Hom.:
0
Cov.:
0
AF XY:
0.000109
AC XY:
58
AN XY:
534516
show subpopulations
Gnomad4 AFR exome
AF:
0.000261
Gnomad4 AMR exome
AF:
0.000765
Gnomad4 ASJ exome
AF:
0.0000670
Gnomad4 EAS exome
AF:
0.00112
Gnomad4 SAS exome
AF:
0.000229
Gnomad4 FIN exome
AF:
0.000165
Gnomad4 NFE exome
AF:
0.0000386
Gnomad4 OTH exome
AF:
0.000117
GnomAD4 genome
AF:
0.000133
AC:
13
AN:
98068
Hom.:
0
Cov.:
0
AF XY:
0.000133
AC XY:
6
AN XY:
45108
show subpopulations
Gnomad4 AFR
AF:
0.000241
Gnomad4 AMR
AF:
0.000121
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000316
Gnomad4 SAS
AF:
0.000339
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000783
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs56314229; hg19: chr7-77006717; API