rs7869905

Variant names:

• chr9-132775997-G-C
• rs7869905
• NM_152572.3:c.1121+16637C>G

Variant summary

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

The NM_152572.3(AK8):​c.1121+16637C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,122 control chromosomes in the GnomAD database, including 29,437 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 0.62 (29437 hom., cov: 33)
• Consequence: AK8 NM_152572.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 5 publications found

Genes affected

AK8 (HGNC:26526): (adenylate kinase 8) Enables AMP binding activity and nucleobase-containing compound kinase activity. Involved in nucleoside diphosphate phosphorylation and nucleoside triphosphate biosynthetic process. Located in 9+2 motile cilium. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AK8	NM_152572.3	c.1121+16637C>G		intron_variant	Intron 11 of 12	ENST00000298545.4	NP_689785.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AK8	ENST00000298545.4	c.1121+16637C>G		intron_variant	Intron 11 of 12	1	NM_152572.3	ENSP00000298545.3
AK8	ENST00000476719.1	n.1558+16637C>G		intron_variant	Intron 10 of 11	5
AK8	ENST00000477396.5	n.2036+16637C>G		intron_variant	Intron 13 of 14	2

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93557 AN: 152004 Hom.: 29416 Cov.: 33

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.615 AC: 93606 AN: 152122 Hom.: 29437 Cov.: 33 AF XY: 0.622 AC XY: 46249 AN XY: 74364

African (AFR) AF: 0.490 AC: 20318 AN: 41496

American (AMR) AF: 0.623 AC: 9520 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2366 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4200 AN: 5166

South Asian (SAS) AF: 0.795 AC: 3833 AN: 4824

European-Finnish (FIN) AF: 0.702 AC: 7424 AN: 10580

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.646 AC: 43931 AN: 67986

Other (OTH) AF: 0.603 AC: 1275 AN: 2114

Alfa AF: 0.625 Hom.: 3696

Bravo AF: 0.599

Asia WGS AF: 0.776 AC: 2696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	11
DANN	Benign	0.70
PhyloP100		1.5
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: rs7869905; hg19: chr9-135651384;