rs12573590

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_006721.4(ADK):​c.65+9715C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0178 in 152,244 control chromosomes in the GnomAD database, including 41 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 0.018 ( 41 hom., cov: 32)

Consequence

ADK
NM_006721.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.450
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0178 (2712/152244) while in subpopulation NFE AF= 0.0256 (1744/68010). AF 95% confidence interval is 0.0246. There are 41 homozygotes in gnomad4. There are 1325 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 2712 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADKNM_006721.4 linkuse as main transcriptc.65+9715C>A intron_variant ENST00000539909.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADKENST00000539909.6 linkuse as main transcriptc.65+9715C>A intron_variant 2 NM_006721.4 P3P55263-1

Frequencies

GnomAD3 genomes
AF:
0.0178
AC:
2712
AN:
152126
Hom.:
41
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00476
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.00812
Gnomad ASJ
AF:
0.0225
Gnomad EAS
AF:
0.0211
Gnomad SAS
AF:
0.0196
Gnomad FIN
AF:
0.0299
Gnomad MID
AF:
0.0222
Gnomad NFE
AF:
0.0256
Gnomad OTH
AF:
0.0183
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0178
AC:
2712
AN:
152244
Hom.:
41
Cov.:
32
AF XY:
0.0178
AC XY:
1325
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.00474
Gnomad4 AMR
AF:
0.00810
Gnomad4 ASJ
AF:
0.0225
Gnomad4 EAS
AF:
0.0214
Gnomad4 SAS
AF:
0.0197
Gnomad4 FIN
AF:
0.0299
Gnomad4 NFE
AF:
0.0256
Gnomad4 OTH
AF:
0.0176
Alfa
AF:
0.0145
Hom.:
3
Bravo
AF:
0.0148
Asia WGS
AF:
0.0180
AC:
62
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
4.7
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12573590; hg19: chr10-75920816; API