rs7924176

Positions:

• chr10-74536031-A-G
• chr10-74536031-A-T

Variant summary

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

The NM_006721.4(ADK):​c.726+10605A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,808 control chromosomes in the GnomAD database, including 9,181 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 0.31 (9181 hom., cov: 30)
• Consequence: ADK NM_006721.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.53

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADK	NM_006721.4	c.726+10605A>G		intron_variant		ENST00000539909.6	NP_006712.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADK	ENST00000539909.6	c.726+10605A>G		intron_variant		2	NM_006721.4	ENSP00000443965	P3

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46619 AN: 151690 Hom.: 9183 Cov.: 30

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.307 AC: 46610 AN: 151808 Hom.: 9181 Cov.: 30 AF XY: 0.300 AC XY: 22270 AN XY: 74156

Gnomad4 AFR AF: 0.0960

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.362

Alfa AF: 0.418 Hom.: 27819

Bravo AF: 0.295

Asia WGS AF: 0.110 AC: 382 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.4
DANN	Benign	0.76

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: rs7924176; hg19: chr10-76295789;