7-91940883-TGGCGGCGGC-TGGCGGCGGCGGCGGCGGC

Variant names:

• chr7-91940883-T-TGGCGGCGGC
• rs371245265
• NM_005751.5:c.-208_-200dupCGGCGGCGG

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_005751.5(AKAP9):​c.-208_-200dupCGGCGGCGG variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00112 in 601,826 control chromosomes in the GnomAD database, including 3 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00093 (0 hom., cov: 34)
  • Exomes 𝑓: 0.0012 (3 hom.)
• Consequence: AKAP9 NM_005751.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.47

Genes affected

AKAP9 (HGNC:379): (A-kinase anchoring protein 9) 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. Alternate splicing of this gene results in at least two isoforms that localize to the centrosome and the Golgi apparatus, and interact with numerous signaling proteins from multiple signal transduction pathways. These signaling proteins include type II protein kinase A, serine/threonine kinase protein kinase N, protein phosphatase 1, protein phosphatase 2a, protein kinase C-epsilon and phosphodiesterase 4D3. [provided by RefSeq, Aug 2008]

LOC124901698 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 141 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AKAP9	NM_005751.5	c.-208_-200dupCGGCGGCGG		5_prime_UTR_variant	Exon 1 of 50	ENST00000356239.8	NP_005742.4
AKAP9	NM_147185.3	c.-208_-200dupCGGCGGCGG		5_prime_UTR_variant	Exon 1 of 50		NP_671714.1
LOC124901698	XR_007060431.1	n.-41_-33dupGCCGCCGCC		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AKAP9	ENST00000356239	c.-208_-200dupCGGCGGCGG		5_prime_UTR_variant	Exon 1 of 50	1	NM_005751.5	ENSP00000348573.3

Frequencies

GnomAD3 genomes AF: 0.000927 AC: 141 AN: 152158 Hom.: 0 Cov.: 34

Gnomad AFR AF: 0.000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000828

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00163

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.00119 AC: 536 AN: 449550 Hom.: 3 Cov.: 4 AF XY: 0.00126 AC XY: 302 AN XY: 239174

Gnomad4 AFR exome AF: 0.000328

Gnomad4 AMR exome AF: 0.000453

Gnomad4 ASJ exome AF: 0.0000744

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000913

Gnomad4 FIN exome AF: 0.000365

Gnomad4 NFE exome AF: 0.00166

Gnomad4 OTH exome AF: 0.000938

GnomAD4 genome AF: 0.000926 AC: 141 AN: 152276 Hom.: 0 Cov.: 34 AF XY: 0.000833 AC XY: 62 AN XY: 74462

Gnomad4 AFR AF: 0.000241

Gnomad4 AMR AF: 0.000653

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000829

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00163

Gnomad4 OTH AF: 0.00142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs371245265; hg19: chr7-91570197;