chr13-42291061-C-G

Position:

• chr13-42291061-C-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
AKAP11	NM_016248.4	c.52-1324C>G		intron_variant		ENST00000025301.4	NP_057332.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AKAP11	ENST00000025301.4	c.52-1324C>G		intron_variant		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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.0670

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0345

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.102

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

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: rs17063155; hg19: chr13-42865197;