rs7808587

chr7-91990782-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005751.5(AKAP9):c.352-1376G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,058 control chromosomes in the GnomAD database, including 26,037 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 0.57 (26037 hom., cov: 33)
• Consequence: AKAP9 NM_005751.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.486

Genes affected

AKAP9 (HGNC:379): (A-kinase anchoring protein 9) 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. Alternate splicing of this gene results in at least two isoforms that localize to the centrosome and the Golgi apparatus, and interact with numerous signaling proteins from multiple signal transduction pathways. These signaling proteins include type II protein kinase A, serine/threonine kinase protein kinase N, protein phosphatase 1, protein phosphatase 2a, protein kinase C-epsilon and phosphodiesterase 4D3. [provided by RefSeq, Aug 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKAP9	NM_005751.5	c.352-1376G>A		intron_variant		ENST00000356239.8
AKAP9	NM_147185.3	c.352-1376G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKAP9	ENST00000356239.8	c.352-1376G>A		intron_variant		1	NM_005751.5	P4

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86642 AN: 151940 Hom.: 25985 Cov.: 33

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.568

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.570 AC: 86747 AN: 152058 Hom.: 26037 Cov.: 33 AF XY: 0.569 AC XY: 42299 AN XY: 74300

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.648

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.533

Gnomad4 FIN AF: 0.476

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.567

Alfa AF: 0.527 Hom.: 6843

Bravo AF: 0.581

Asia WGS AF: 0.547 AC: 1902 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	3.0
Dann	Benign	0.57

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

LitVar

Other links and lift over

dbSNP: rs7808587; hg19: chr7-91620096;