NM_152572.3:c.1122-29572C>T

Variant names:

• chr9-132757106-G-A
• rs12552369
• NM_152572.3:c.1122-29572C>T

Variant summary

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

The NM_152572.3(AK8):​c.1122-29572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 152,040 control chromosomes in the GnomAD database, including 13,806 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 0.38 (13806 hom., cov: 33)
• Consequence: AK8 NM_152572.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630
• Publications: 7 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AK8	NM_152572.3	c.1122-29572C>T		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.1122-29572C>T		intron_variant	Intron 11 of 12	1	NM_152572.3	ENSP00000298545.3
AK8	ENST00000476719.1	n.1559-29572C>T		intron_variant	Intron 10 of 11	5
AK8	ENST00000477396.5	n.2037-29572C>T		intron_variant	Intron 13 of 14	2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58306 AN: 151922 Hom.: 13788 Cov.: 33

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.384 AC: 58332 AN: 152040 Hom.: 13806 Cov.: 33 AF XY: 0.391 AC XY: 29039 AN XY: 74312

African (AFR) AF: 0.0958 AC: 3982 AN: 41552

American (AMR) AF: 0.491 AC: 7501 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1907 AN: 3368

East Asian (EAS) AF: 0.344 AC: 1784 AN: 5184

South Asian (SAS) AF: 0.488 AC: 2352 AN: 4822

European-Finnish (FIN) AF: 0.542 AC: 5726 AN: 10566

Middle Eastern (MID) AF: 0.400 AC: 116 AN: 290

European-Non Finnish (NFE) AF: 0.493 AC: 33478 AN: 67960

Other (OTH) AF: 0.402 AC: 846 AN: 2104

Alfa AF: 0.434 Hom.: 22230

Bravo AF: 0.364

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.98
DANN	Benign	0.88
PhyloP100		-0.63
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: rs12552369; hg19: chr9-135632493;