chr17-19941867-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_007202.4(AKAP10):c.1020C>T(p.Phe340=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,610,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
AKAP10
NM_007202.4 synonymous
NM_007202.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.187
Genes affected
AKAP10 (HGNC:368): (A-kinase anchoring protein 10) This gene encodes a member of the A-kinase anchor protein family. A-kinase anchor proteins bind to the regulatory subunits of protein kinase A (PKA) and confine the holoenzyme to discrete locations within the cell. The encoded protein is localized to mitochondria and interacts with both the type I and type II regulatory subunits of PKA. Polymorphisms in this gene may be associated with increased risk of arrhythmias and sudden cardiac death. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 17-19941867-G-A is Benign according to our data. Variant chr17-19941867-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3040781.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.187 with no splicing effect.
BS2
?
High AC in GnomAdExome at 5 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP10 | NM_007202.4 | c.1020C>T | p.Phe340= | synonymous_variant | 6/15 | ENST00000225737.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP10 | ENST00000225737.11 | c.1020C>T | p.Phe340= | synonymous_variant | 6/15 | 1 | NM_007202.4 | P1 | |
AKAP10 | ENST00000395536.7 | c.1020C>T | p.Phe340= | synonymous_variant | 6/14 | 5 | |||
AKAP10 | ENST00000460046.2 | c.114C>T | p.Phe38= | synonymous_variant, NMD_transcript_variant | 2/4 | 3 | |||
AKAP10 | ENST00000582611.5 | c.*563C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152144Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248878Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134584
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GnomAD4 exome AF: 0.0000178 AC: 26AN: 1458096Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 725234
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
AKAP10-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 23, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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