14-32813264-C-A

Variant names:

• chr14-32813264-C-A
• rs2383378
• NM_004274.5:c.3589-8138C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004274.5(AKAP6):​c.3589-8138C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,990 control chromosomes in the GnomAD database, including 8,129 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 0.29 (8129 hom., cov: 31)
• Consequence: AKAP6 NM_004274.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 14 publications found

Genes affected

AKAP6 (HGNC:376): (A-kinase anchoring protein 6) 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. The encoded protein is highly expressed in various brain regions and cardiac and skeletal muscle. It is specifically localized to the sarcoplasmic reticulum and nuclear membrane, and is involved in anchoring PKA to the nuclear membrane or sarcoplasmic reticulum. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004274.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKAP6	NM_004274.5	MANE Select	c.3589-8138C>A		intron	N/A	NP_004265.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKAP6	ENST00000280979.9	TSL:1 MANE Select	c.3589-8138C>A		intron	N/A	ENSP00000280979.4
	AKAP6	ENST00000557272.1	TSL:5	c.3589-16584C>A		intron	N/A	ENSP00000451247.1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44808 AN: 151874 Hom.: 8125 Cov.: 31

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.295 AC: 44821 AN: 151990 Hom.: 8129 Cov.: 31 AF XY: 0.293 AC XY: 21730 AN XY: 74286

African (AFR) AF: 0.0908 AC: 3768 AN: 41476

American (AMR) AF: 0.331 AC: 5048 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3468

East Asian (EAS) AF: 0.126 AC: 650 AN: 5164

South Asian (SAS) AF: 0.286 AC: 1376 AN: 4818

European-Finnish (FIN) AF: 0.382 AC: 4029 AN: 10556

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27507 AN: 67936

Other (OTH) AF: 0.325 AC: 684 AN: 2104

Alfa AF: 0.353 Hom.: 23088

Bravo AF: 0.279

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.32
DANN	Benign	0.35
PhyloP100		-1.4
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

Other links and lift over

dbSNP: rs2383378; hg19: chr14-33282470;