rs17080959

Variant names:

• chr6-151254809-C-T
• rs17080959
• NM_005100.4:c.162+14085C>T

Variant summary

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

The NM_005100.4(AKAP12):​c.162+14085C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,164 control chromosomes in the GnomAD database, including 1,857 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 0.15 (1857 hom., cov: 34)
• Consequence: AKAP12 NM_005100.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0970
• Publications: 6 publications found

Genes affected

AKAP12 (HGNC:370): (A-kinase anchoring protein 12) 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 expressed in endothelial cells, cultured fibroblasts, and osteosarcoma cells. It associates with protein kinases A and C and phosphatase, and serves as a scaffold protein in signal transduction. This protein and RII PKA colocalize at the cell periphery. This protein is a cell growth-related protein. Antibodies to this protein can be produced by patients with myasthenia gravis. Alternative splicing of this gene results in two transcript variants encoding different isoforms. [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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP12	NM_005100.4	c.162+14085C>T		intron_variant	Intron 2 of 4	ENST00000402676.7	NP_005091.2
AKAP12	XM_017011517.3	c.162+14085C>T		intron_variant	Intron 2 of 4		XP_016867006.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKAP12	ENST00000402676.7	c.162+14085C>T		intron_variant	Intron 2 of 4	5	NM_005100.4	ENSP00000384537.2
AKAP12	ENST00000253332.5	c.162+14085C>T		intron_variant	Intron 1 of 3	1		ENSP00000253332.1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23226 AN: 152046 Hom.: 1853 Cov.: 34

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0752

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.153 AC: 23259 AN: 152164 Hom.: 1857 Cov.: 34 AF XY: 0.156 AC XY: 11596 AN XY: 74388

African (AFR) AF: 0.170 AC: 7043 AN: 41512

American (AMR) AF: 0.122 AC: 1858 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3470

East Asian (EAS) AF: 0.159 AC: 821 AN: 5178

South Asian (SAS) AF: 0.0754 AC: 364 AN: 4826

European-Finnish (FIN) AF: 0.240 AC: 2539 AN: 10574

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9591 AN: 68010

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.142 Hom.: 2559

Bravo AF: 0.148

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.55
PhyloP100		-0.097
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: rs17080959; hg19: chr6-151575944; COSMIC: COSV53571809;