rs11001109

chr10-74683339-A-G

Variant summary

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

The NM_006721.4(ADK):c.964+13070A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,022 control chromosomes in the GnomAD database, including 35,360 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 0.68 (35360 hom., cov: 32)
• Consequence: ADK NM_006721.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

ADK (HGNC:257): (adenosine kinase) This gene an enzyme which catalyzes the transfer of the gamma-phosphate from ATP to adenosine, thereby serving as a regulator of concentrations of both extracellular adenosine and intracellular adenine nucleotides. Adenosine has widespread effects on the cardiovascular, nervous, respiratory, and immune systems and inhibitors of the enzyme could play an important pharmacological role in increasing intravascular adenosine concentrations and acting as anti-inflammatory agents. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADK	NM_006721.4	c.964+13070A>G		intron_variant		ENST00000539909.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADK	ENST00000539909.6	c.964+13070A>G		intron_variant		2	NM_006721.4	P3

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103122 AN: 151904 Hom.: 35345 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.688

Gnomad ASJ AF: 0.791

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.679 AC: 103183 AN: 152022 Hom.: 35360 Cov.: 32 AF XY: 0.678 AC XY: 50378 AN XY: 74306

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.688

Gnomad4 ASJ AF: 0.791

Gnomad4 EAS AF: 0.709

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.706

Alfa AF: 0.684 Hom.: 4488

Bravo AF: 0.680

Asia WGS AF: 0.683 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.2
Dann	Benign	0.64

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: rs11001109; hg19: chr10-76443097;