7-91940940-G-A
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005751.5(AKAP9):c.-160G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000407 in 769,588 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.00032 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00043 ( 1 hom. )
Consequence
AKAP9
NM_005751.5 5_prime_UTR
NM_005751.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.91
Genes affected
AKAP9 (HGNC:379): (A-kinase anchoring protein 9) The A-kinase anchor proteins (AKAPs) are a group of structurally diverse proteins which have the common function of binding to the regulatory subunit of protein kinase A (PKA) and confining the holoenzyme to discrete locations within the cell. This gene encodes a member of the AKAP family. Alternate splicing of this gene results in at least two isoforms that localize to the centrosome and the Golgi apparatus, and interact with numerous signaling proteins from multiple signal transduction pathways. These signaling proteins include type II protein kinase A, serine/threonine kinase protein kinase N, protein phosphatase 1, protein phosphatase 2a, protein kinase C-epsilon and phosphodiesterase 4D3. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 49 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| AKAP9 | NM_005751.5 | c.-160G>A | 5_prime_UTR_variant | 1/50 | ENST00000356239.8 | ||
| AKAP9 | NM_147185.3 | c.-160G>A | 5_prime_UTR_variant | 1/50 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AKAP9 | ENST00000356239.8 | c.-160G>A | 5_prime_UTR_variant | 1/50 | 1 | NM_005751.5 | P4 |
Frequencies
GnomAD3 genomes 0.000322 AC: 49AN: 152284Hom.: 0 Cov.: 34
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GnomAD4 exome AF: 0.000428 AC: 264AN: 617304Hom.: 1 Cov.: 8 AF XY: 0.000443 AC XY: 146AN XY: 329280
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GnomAD4 genome 0.000322 AC: 49AN: 152284Hom.: 0 Cov.: 34 AF XY: 0.000296 AC XY: 22AN XY: 74402
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Long QT syndrome 11 Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 20, 2021 | - - |
Congenital long QT syndrome Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
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DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -3
Find out detailed SpliceAI scores and Pangolin per-transcript scores at