chr17-57106116-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_003488.4(AKAP1):c.652G>A(p.Ala218Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00871 in 1,606,984 control chromosomes in the GnomAD database, including 65 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0086 ( 6 hom., cov: 33)
Exomes 𝑓: 0.0087 ( 59 hom. )
Consequence
AKAP1
NM_003488.4 missense
NM_003488.4 missense
Scores
17
Clinical Significance
Conservation
PhyloP100: 1.39
Genes affected
AKAP1 (HGNC:367): (A-kinase anchoring protein 1) 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. The encoded protein binds to type I and type II regulatory subunits of PKA and anchors them to the mitochondrion. This protein is speculated to be involved in the cAMP-dependent signal transduction pathway and in directing RNA to a specific cellular compartment. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0032155812).
BP6
?
Variant 17-57106116-G-A is Benign according to our data. Variant chr17-57106116-G-A is described in ClinVar as [Benign]. Clinvar id is 777890.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 1299 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP1 | NM_003488.4 | c.652G>A | p.Ala218Thr | missense_variant | 2/11 | ENST00000337714.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP1 | ENST00000337714.8 | c.652G>A | p.Ala218Thr | missense_variant | 2/11 | 1 | NM_003488.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00853 AC: 1299AN: 152220Hom.: 6 Cov.: 33
GnomAD3 genomes
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GnomAD3 exomes AF: 0.00706 AC: 1743AN: 246838Hom.: 11 AF XY: 0.00702 AC XY: 936AN XY: 133328
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GnomAD4 exome AF: 0.00873 AC: 12699AN: 1454646Hom.: 59 Cov.: 92 AF XY: 0.00864 AC XY: 6245AN XY: 722714
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GnomAD4 genome ? AF: 0.00856 AC: 1304AN: 152338Hom.: 6 Cov.: 33 AF XY: 0.00819 AC XY: 610AN XY: 74500
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ESP6500AA
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Asia WGS
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3478
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 31, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;T;T;T;T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N;N;N;N;.
MutationTaster
Benign
N;N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;.;.;.;N;N;.
REVEL
Benign
Sift
Benign
T;.;.;.;T;T;.
Sift4G
Benign
T;T;T;T;T;D;D
Polyphen
B;B;B;B;B;.;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at