dbSNP rs3903759: AKAP7:c.702+281C>A (chr6-131199854-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_016377.4(AKAP7):c.702+281C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 377,446 control chromosomes in the GnomAD database, including 3,636 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 0.12 ( 1318 hom., cov: 32)

Exomes 𝑓: 0.14 ( 2318 hom. )

Consequence

AKAP7
NM_016377.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.184

Publications

14 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]

AKAP7 links:

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=-0.78).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP7	NM_016377.4 link	c.702+281C>A		intron_variant	Intron 6 of 7	ENST00000431975.7	NP_057461.2	Q9P0M2-1Q2TAJ5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKAP7	ENST00000431975.7 link	c.702+281C>A		intron_variant	Intron 6 of 7	2	NM_016377.4	ENSP00000405252.2		Q9P0M2-1

Frequencies

GnomAD3 genomes

AF:

0.120

AC:

18239

AN:

152068

Hom.:

1318

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0747

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.0760

Gnomad ASJ

AF:

0.0832

Gnomad EAS

AF:

0.0410

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.216

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.148

Gnomad OTH

AF:

0.113

GnomAD4 exome

AF:

0.135

AC:

30461

AN:

225260

Hom.:

2318

AF XY:

0.135

AC XY:

16260

AN XY:

120306

show subpopulations

African (AFR)

AF:

0.0630

AC:

300

AN:

4764

American (AMR)

AF:

0.0670

AC:

287

AN:

4286

Ashkenazi Jewish (ASJ)

AF:

0.0750

AC:

519

AN:

6924

East Asian (EAS)

AF:

0.0132

AC:

131

AN:

9938

South Asian (SAS)

AF:

0.144

AC:

4212

AN:

29182

European-Finnish (FIN)

AF:

0.217

AC:

3113

AN:

14322

Middle Eastern (MID)

AF:

0.0876

AC:

AN:

970

European-Non Finnish (NFE)

AF:

0.143

AC:

20179

AN:

141386

Other (OTH)

AF:

0.121

AC:

1635

AN:

13488

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.489

Heterozygous variant carriers

1208

2416

3624

4832

6040

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

116

174

232

290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.120

AC:

18239

AN:

152186

Hom.:

1318

Cov.:

AF XY:

0.121

AC XY:

8989

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.0746

AC:

3099

AN:

41528

American (AMR)

AF:

0.0759

AC:

1160

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.0832

AC:

289

AN:

3472

East Asian (EAS)

AF:

0.0406

AC:

210

AN:

5178

South Asian (SAS)

AF:

0.129

AC:

623

AN:

4816

European-Finnish (FIN)

AF:

0.216

AC:

2290

AN:

10592

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.148

AC:

10089

AN:

67990

Other (OTH)

AF:

0.112

AC:

237

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

810

1621

2431

3242

4052

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

220

440

660

880

1100

<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:

0.133

Hom.:

2521

Bravo

AF:

0.105

Asia WGS

AF:

0.0780

AC:

273

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

7.2

(source)

DANN

Benign

0.71

PhyloP100

-0.18

PromoterAI

-0.46

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over