chr6-131181488-G-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016377.4(AKAP7):​c.589+12215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0142 in 152,256 control chromosomes in the GnomAD database, including 145 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.014 ( 145 hom., cov: 32)

Consequence

AKAP7
NM_016377.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.71

Publications

2 publications found
Variant links:
Genes affected
AKAP7 (HGNC:377): (A-kinase anchoring protein 7) This gene encodes a member of the A-kinase anchoring protein (AKAP) family, a group of functionally related proteins that bind to a regulatory subunit (RII) of cAMP-dependent protein kinase A (PKA) and target the enzyme to specific subcellular compartments. AKAPs have a common RII-binding domain, but contain different targeting motifs responsible for directing PKA to distinct intracellular locations. Three alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Apr 2011]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AKAP7NM_016377.4 linkc.589+12215G>A intron_variant Intron 5 of 7 ENST00000431975.7 NP_057461.2 Q9P0M2-1Q2TAJ5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AKAP7ENST00000431975.7 linkc.589+12215G>A intron_variant Intron 5 of 7 2 NM_016377.4 ENSP00000405252.2 Q9P0M2-1

Frequencies

GnomAD3 genomes
AF:
0.0141
AC:
2150
AN:
152138
Hom.:
143
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00176
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0660
Gnomad ASJ
AF:
0.00432
Gnomad EAS
AF:
0.176
Gnomad SAS
AF:
0.00642
Gnomad FIN
AF:
0.00425
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000470
Gnomad OTH
AF:
0.0148
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0142
AC:
2162
AN:
152256
Hom.:
145
Cov.:
32
AF XY:
0.0156
AC XY:
1163
AN XY:
74446
show subpopulations
African (AFR)
AF:
0.00176
AC:
73
AN:
41536
American (AMR)
AF:
0.0668
AC:
1021
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.00432
AC:
15
AN:
3470
East Asian (EAS)
AF:
0.176
AC:
911
AN:
5182
South Asian (SAS)
AF:
0.00643
AC:
31
AN:
4824
European-Finnish (FIN)
AF:
0.00425
AC:
45
AN:
10596
Middle Eastern (MID)
AF:
0.00340
AC:
1
AN:
294
European-Non Finnish (NFE)
AF:
0.000470
AC:
32
AN:
68034
Other (OTH)
AF:
0.0156
AC:
33
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
98
196
293
391
489
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
26
52
78
104
130
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0177
Hom.:
22
Bravo
AF:
0.0216
Asia WGS
AF:
0.0770
AC:
269
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.94
CADD
Benign
0.15
DANN
Benign
0.43
PhyloP100
-1.7
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs17060099; hg19: chr6-131502628; API