rs17522122

Variant names:

• chr14-32833676-G-T
• rs17522122
• NM_004274.5:c.*3871G>T

Variant summary

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

The ENST00000280979.9(AKAP6):​c.*3871G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,934 control chromosomes in the GnomAD database, including 13,664 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 0.42 (13664 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: AKAP6 ENST00000280979.9 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 37 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]

ENSG00000302430 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000280979.9. 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.*3871G>T		3_prime_UTR	Exon 14 of 14	NP_004265.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AKAP6	ENST00000280979.9	TSL:1 MANE Select	c.*3871G>T		3_prime_UTR	Exon 14 of 14	ENSP00000280979.4
	ENSG00000302430	ENST00000786608.1		n.278+8610C>A		intron	N/A
	ENSG00000302430	ENST00000786609.1		n.214+5164C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63108 AN: 151816 Hom.: 13650 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.435

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.416 AC: 63140 AN: 151934 Hom.: 13664 Cov.: 32 AF XY: 0.413 AC XY: 30643 AN XY: 74232

African (AFR) AF: 0.299 AC: 12384 AN: 41434

American (AMR) AF: 0.403 AC: 6161 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1645 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1915 AN: 5164

South Asian (SAS) AF: 0.447 AC: 2151 AN: 4814

European-Finnish (FIN) AF: 0.458 AC: 4810 AN: 10506

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32619 AN: 67944

Other (OTH) AF: 0.442 AC: 934 AN: 2112

Alfa AF: 0.446 Hom.: 24074

Bravo AF: 0.403

Asia WGS AF: 0.477 AC: 1656 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.34
PhyloP100		0.26

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: rs17522122; hg19: chr14-33302882;