rs9400317

chr6-109686444-A-Gchr6-109686444-A-T

Variant summary

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

The NM_001145128.3(AK9):c.-12+4703T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.911 in 152,284 control chromosomes in the GnomAD database, including 63,370 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 0.91 (63370 hom., cov: 32)
• Consequence: AK9 NM_001145128.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

Genes affected

AK9 (HGNC:33814): (adenylate kinase 9) The protein encoded by this gene catalyzes the interconversion of nucleosides, possessing both nucleoside monophosphate and diphosphate kinase activities. The encoded protein uses these interconversions to maintain nucleoside homeostasis. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AK9	NM_001145128.3	c.-12+4703T>C		intron_variant		ENST00000424296.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AK9	ENST00000424296.7	c.-12+4703T>C		intron_variant		5	NM_001145128.3	P1

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138586 AN: 152166 Hom.: 63309 Cov.: 32

Gnomad AFR AF: 0.980

Gnomad AMI AF: 0.866

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.911 AC: 138705 AN: 152284 Hom.: 63370 Cov.: 32 AF XY: 0.912 AC XY: 67871 AN XY: 74448

Gnomad4 AFR AF: 0.980

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.856

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.888

Alfa AF: 0.876 Hom.: 122583

Bravo AF: 0.917

Asia WGS AF: 0.950 AC: 3306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	6.8
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: rs9400317; hg19: chr6-110007647;