rs6558295
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003801.4(GPAA1):c.1010+10C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0886 in 1,607,866 control chromosomes in the GnomAD database, including 8,725 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.14 ( 2291 hom., cov: 33)
Exomes 𝑓: 0.083 ( 6434 hom. )
Consequence
GPAA1
NM_003801.4 intron
NM_003801.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.123
Genes affected
GPAA1 (HGNC:4446): (glycosylphosphatidylinositol anchor attachment 1) Posttranslational glycosylphosphatidylinositol (GPI) anchor attachment serves as a general mechanism for linking proteins to the cell surface membrane. The protein encoded by this gene presumably functions in GPI anchoring at the GPI transfer step. The mRNA transcript is ubiquitously expressed in both fetal and adult tissues. The anchor attachment protein 1 contains an N-terminal signal sequence, 1 cAMP- and cGMP-dependent protein kinase phosphorylation site, 1 leucine zipper pattern, 2 potential N-glycosylation sites, and 8 putative transmembrane domains. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 8-144084619-C-G is Benign according to our data. Variant chr8-144084619-C-G is described in ClinVar as [Benign]. Clinvar id is 1300876.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPAA1 | NM_003801.4 | c.1010+10C>G | intron_variant | ENST00000355091.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPAA1 | ENST00000355091.9 | c.1010+10C>G | intron_variant | 1 | NM_003801.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.138 AC: 20977AN: 152132Hom.: 2283 Cov.: 33
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GnomAD3 exomes AF: 0.0809 AC: 20034AN: 247792Hom.: 1380 AF XY: 0.0763 AC XY: 10251AN XY: 134426
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GnomAD4 exome AF: 0.0834 AC: 121364AN: 1455616Hom.: 6434 Cov.: 33 AF XY: 0.0813 AC XY: 58765AN XY: 723232
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GnomAD4 genome ? AF: 0.138 AC: 21020AN: 152250Hom.: 2291 Cov.: 33 AF XY: 0.134 AC XY: 9994AN XY: 74440
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 21, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at