chr17-19931799-C-T
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_007202.4(AKAP10):c.1641+6G>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 1,611,352 control chromosomes in the GnomAD database, including 11,952 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.095 ( 788 hom., cov: 31)
Exomes 𝑓: 0.12 ( 11164 hom. )
Consequence
AKAP10
NM_007202.4 splice_donor_region, intron
NM_007202.4 splice_donor_region, intron
Scores
2
Splicing: ADA: 0.0002518
2
Clinical Significance
Conservation
PhyloP100: -1.14
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 17-19931799-C-T is Benign according to our data. Variant chr17-19931799-C-T is described in ClinVar as [Benign]. Clinvar id is 3055540.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AKAP10 | NM_007202.4 | c.1641+6G>A | splice_donor_region_variant, intron_variant | ENST00000225737.11 | |||
AKAP10 | NM_001330152.2 | c.1467+4487G>A | intron_variant | ||||
AKAP10 | XR_007065258.1 | n.1790+6G>A | splice_donor_region_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AKAP10 | ENST00000225737.11 | c.1641+6G>A | splice_donor_region_variant, intron_variant | 1 | NM_007202.4 | P1 | |||
AKAP10 | ENST00000395536.7 | c.1467+4487G>A | intron_variant | 5 | |||||
AKAP10 | ENST00000583951.1 | c.62+6G>A | splice_donor_region_variant, intron_variant | 3 | |||||
AKAP10 | ENST00000578898.1 | c.73+6G>A | splice_donor_region_variant, intron_variant, NMD_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0948 AC: 14407AN: 152008Hom.: 784 Cov.: 31
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GnomAD3 exomes AF: 0.106 AC: 26466AN: 248790Hom.: 1570 AF XY: 0.106 AC XY: 14212AN XY: 134366
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GnomAD4 exome AF: 0.121 AC: 176387AN: 1459228Hom.: 11164 Cov.: 31 AF XY: 0.119 AC XY: 86654AN XY: 725778
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GnomAD4 genome AF: 0.0948 AC: 14420AN: 152124Hom.: 788 Cov.: 31 AF XY: 0.0943 AC XY: 7011AN XY: 74370
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
AKAP10-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 2019 | This variant is classified as 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
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at