9-132742896-A-G

Position:

• chr9-132742896-A-G

Variant summary

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

The NM_152572.3(AK8):​c.1122-15362T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 152,138 control chromosomes in the GnomAD database, including 9,552 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 0.34 (9552 hom., cov: 33)
• Consequence: AK8 NM_152572.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AK8	NM_152572.3	c.1122-15362T>C		intron_variant		ENST00000298545.4	NP_689785.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AK8	ENST00000298545.4	c.1122-15362T>C		intron_variant		1	NM_152572.3	ENSP00000298545	P1
AK8	ENST00000476719.1	n.1559-15362T>C		intron_variant, non_coding_transcript_variant		5
AK8	ENST00000477396.5	n.2037-15362T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.336 AC: 51112 AN: 152020 Hom.: 9548 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.379

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

GnomAD4 genome AF: 0.336 AC: 51121 AN: 152138 Hom.: 9552 Cov.: 33 AF XY: 0.341 AC XY: 25339 AN XY: 74382

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.430

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.384

Alfa AF: 0.396 Hom.: 14205

Bravo AF: 0.314

Asia WGS AF: 0.471 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.1
DANN	Benign	0.77

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: rs11243897; hg19: chr9-135618283;