7-77377400-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAA

Position:

• chr7-77377400-CAAAAAAAAAAAA-CAAAAAAAAAAAAAAAAAAAAAAA

Variant summary

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

The NM_017439.4(GSAP):​c.577-11_577-10insTTTTTTTTTTT variant causes a splice polypyrimidine tract, 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 0.00049 (0 hom., cov: 0)
  • Exomes 𝑓: 0.000079 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GSAP NM_017439.4 splice_polypyrimidine_tract, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GSAP	NM_017439.4	c.577-11_577-10insTTTTTTTTTTT		splice_polypyrimidine_tract_variant, intron_variant		ENST00000257626.12	NP_059135.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSAP	ENST00000257626.12	c.577-11_577-10insTTTTTTTTTTT		splice_polypyrimidine_tract_variant, intron_variant		1	NM_017439.4	ENSP00000257626	P1
GSAP	ENST00000334003.11	n.468-11_468-10insTTTTTTTTTTT		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.000479 AC: 47 AN: 98042 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000364

Gnomad ASJ AF: 0.000375

Gnomad EAS AF: 0.00159

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000215

Gnomad OTH AF: 0.000786

GnomAD4 exome AF: 0.0000792 AC: 86 AN: 1086464 Hom.: 0 Cov.: 0 AF XY: 0.0000954 AC XY: 51 AN XY: 534566

Gnomad4 AFR exome AF: 0.000218

Gnomad4 AMR exome AF: 0.000622

Gnomad4 ASJ exome AF: 0.0000670

Gnomad4 EAS exome AF: 0.000957

Gnomad4 SAS exome AF: 0.000133

Gnomad4 FIN exome AF: 0.0000827

Gnomad4 NFE exome AF: 0.0000386

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000490 AC: 48 AN: 98046 Hom.: 0 Cov.: 0 AF XY: 0.000488 AC XY: 22 AN XY: 45110

Gnomad4 AFR AF: 0.00104

Gnomad4 AMR AF: 0.000485

Gnomad4 ASJ AF: 0.000375

Gnomad4 EAS AF: 0.00159

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000215

Gnomad4 OTH AF: 0.000786

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56314229; hg19: chr7-77006717;