XM_017011509.2:c.-116C>G

Variant names:

• chr6-131125651-C-G
• rs602848
• XM_017011509.2:c.-116C>G

Variant summary

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

The XM_017011509.2(AKAP7):​c.-116C>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 152,140 control chromosomes in the GnomAD database, including 46,414 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 0.77 (46414 hom., cov: 32)
• Consequence: AKAP7 XM_017011509.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.929
• Publications: 8 publications found

Genes affected

AKAP7 (HGNC:377): (A-kinase anchoring protein 7) This gene encodes a member of the A-kinase anchoring protein (AKAP) family, a group of functionally related proteins that bind to a regulatory subunit (RII) of cAMP-dependent protein kinase A (PKA) and target the enzyme to specific subcellular compartments. AKAPs have a common RII-binding domain, but contain different targeting motifs responsible for directing PKA to distinct intracellular locations. Three alternatively spliced transcript variants encoding different isoforms have been described.[provided by RefSeq, Apr 2011]

ENSG00000288977 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000690501.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288977	ENST00000690501.2		n.50C>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288977	ENST00000771407.1		n.31C>G		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117816 AN: 152022 Hom.: 46379 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.743

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.771

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

GnomAD4 genome AF: 0.775 AC: 117906 AN: 152140 Hom.: 46414 Cov.: 32 AF XY: 0.780 AC XY: 58048 AN XY: 74392

African (AFR) AF: 0.652 AC: 27015 AN: 41454

American (AMR) AF: 0.792 AC: 12120 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2712 AN: 3472

East Asian (EAS) AF: 0.981 AC: 5079 AN: 5178

South Asian (SAS) AF: 0.770 AC: 3712 AN: 4820

European-Finnish (FIN) AF: 0.919 AC: 9740 AN: 10602

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.809 AC: 55021 AN: 68002

Other (OTH) AF: 0.773 AC: 1635 AN: 2114

Alfa AF: 0.760 Hom.: 2441

Bravo AF: 0.763

Asia WGS AF: 0.880 AC: 3057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.45
DANN	Benign	0.80
PhyloP100		-0.93

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs602848; hg19: chr6-131446791;