rs4629710

chr6-131242437-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016377.4(AKAP7):c.850+22629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 151,596 control chromosomes in the GnomAD database, including 1,850 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 0.14 (1850 hom., cov: 31)
• Consequence: AKAP7 NM_016377.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.719

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AKAP7	NM_016377.4	c.850+22629G>A		intron_variant		ENST00000431975.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AKAP7	ENST00000431975.7	c.850+22629G>A		intron_variant		2	NM_016377.4	P1
	ENST00000702750.1	n.339-24529C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21169 AN: 151492 Hom.: 1850 Cov.: 31

Gnomad AFR AF: 0.0496

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.140 AC: 21164 AN: 151596 Hom.: 1850 Cov.: 31 AF XY: 0.135 AC XY: 10033 AN XY: 74080

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.165

Alfa AF: 0.195 Hom.: 5592

Bravo AF: 0.140

Asia WGS AF: 0.0750 AC: 262 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.22

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: rs4629710; hg19: chr6-131563577;