rs2383378

Positions:

• chr14-32813264-C-A
• chr14-32813264-C-G
• chr14-32813264-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AKAP6	NM_004274.5	c.3589-8138C>A		intron_variant		ENST00000280979.9	NP_004265.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKAP6	ENST00000280979.9	c.3589-8138C>A		intron_variant		1	NM_004274.5	ENSP00000280979.4
AKAP6	ENST00000557272.1	c.3589-16584C>A		intron_variant		5		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

Gnomad4 AFR AF: 0.0908

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.325

Alfa AF: 0.379 Hom.: 15841

Bravo AF: 0.279

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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: rs2383378; hg19: chr14-33282470;