NM_017439.4:c.577-12_577-11dupTT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2

The NM_017439.4(GSAP):​c.577-12_577-11dupTT 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 0.013 ( 27 hom., cov: 0)
Exomes 𝑓: 0.0044 ( 2 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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0132 (1295/98022) while in subpopulation AMR AF= 0.0383 (316/8246). AF 95% confidence interval is 0.0348. There are 27 homozygotes in gnomad4. There are 629 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 27 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GSAPNM_017439.4 linkc.577-12_577-11dupTT 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_577-10insTT intron_variant Intron 8 of 30 1 NM_017439.4 ENSP00000257626.7 A4D1B5-1
GSAPENST00000334003.11 linkn.468-11_468-10insTT intron_variant Intron 7 of 18 2

Frequencies

GnomAD3 genomes
AF:
0.0132
AC:
1297
AN:
98020
Hom.:
27
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0238
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0386
Gnomad ASJ
AF:
0.00412
Gnomad EAS
AF:
0.0245
Gnomad SAS
AF:
0.00780
Gnomad FIN
AF:
0.000339
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00509
Gnomad OTH
AF:
0.0118
GnomAD4 exome
AF:
0.00437
AC:
4731
AN:
1082486
Hom.:
2
Cov.:
0
AF XY:
0.00429
AC XY:
2284
AN XY:
532692
show subpopulations
Gnomad4 AFR exome
AF:
0.0139
Gnomad4 AMR exome
AF:
0.0137
Gnomad4 ASJ exome
AF:
0.00329
Gnomad4 EAS exome
AF:
0.0236
Gnomad4 SAS exome
AF:
0.00560
Gnomad4 FIN exome
AF:
0.00352
Gnomad4 NFE exome
AF:
0.00331
Gnomad4 OTH exome
AF:
0.00525
GnomAD4 genome
AF:
0.0132
AC:
1295
AN:
98022
Hom.:
27
Cov.:
0
AF XY:
0.0139
AC XY:
629
AN XY:
45102
show subpopulations
Gnomad4 AFR
AF:
0.0238
Gnomad4 AMR
AF:
0.0383
Gnomad4 ASJ
AF:
0.00412
Gnomad4 EAS
AF:
0.0246
Gnomad4 SAS
AF:
0.00750
Gnomad4 FIN
AF:
0.000339
Gnomad4 NFE
AF:
0.00509
Gnomad4 OTH
AF:
0.0118

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