rs17063155

Variant names:

• chr13-42291061-C-G
• rs17063155
• NM_016248.4:c.52-1324C>G

Variant summary

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

The NM_016248.4(AKAP11):​c.52-1324C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 151,978 control chromosomes in the GnomAD database, including 1,247 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 0.12 (1247 hom., cov: 32)
• Consequence: AKAP11 NM_016248.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.660
• Publications: 1 publications found

Genes affected

AKAP11 (HGNC:369): (A-kinase anchoring protein 11) 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 at high levels throughout spermatogenesis and in mature sperm. It binds the RI and RII subunits of PKA in testis. It may serve a function in cell cycle control of both somatic cells and germ cells in addition to its putative role in spermatogenesis and sperm function. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP11	NM_016248.4	c.52-1324C>G		intron_variant	Intron 3 of 12	ENST00000025301.4	NP_057332.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKAP11	ENST00000025301.4	c.52-1324C>G		intron_variant	Intron 3 of 12	1	NM_016248.4	ENSP00000025301.2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18653 AN: 151860 Hom.: 1247 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0624

Gnomad ASJ AF: 0.0670

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0347

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.123 AC: 18665 AN: 151978 Hom.: 1247 Cov.: 32 AF XY: 0.120 AC XY: 8919 AN XY: 74258

African (AFR) AF: 0.139 AC: 5771 AN: 41436

American (AMR) AF: 0.0622 AC: 950 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0670 AC: 232 AN: 3464

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0345 AC: 166 AN: 4806

European-Finnish (FIN) AF: 0.185 AC: 1953 AN: 10532

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9205 AN: 67962

Other (OTH) AF: 0.102 AC: 215 AN: 2114

Alfa AF: 0.138 Hom.: 181

Bravo AF: 0.115

Asia WGS AF: 0.0280 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.68
DANN	Benign	0.35
PhyloP100		-0.66
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: rs17063155; hg19: chr13-42865197;