rs7869905

chr9-132775997-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
AK8	NM_152572.3	c.1121+16637C>G		intron_variant		ENST00000298545.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AK8	ENST00000298545.4	c.1121+16637C>G		intron_variant		1	NM_152572.3	P1
AK8	ENST00000476719.1	n.1558+16637C>G		intron_variant, non_coding_transcript_variant		5
AK8	ENST00000477396.5	n.2036+16637C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.681

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.795

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.603

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

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: rs7869905; hg19: chr9-135651384;