rs11000911

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006721.4(ADK):​c.66-13958T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,036 control chromosomes in the GnomAD database, including 22,728 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 0.53 ( 22728 hom., cov: 32)

Consequence

ADK
NM_006721.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.584
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).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ADKNM_006721.4 linkc.66-13958T>C intron_variant ENST00000539909.6 NP_006712.2 P55263-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ADKENST00000539909.6 linkc.66-13958T>C intron_variant 2 NM_006721.4 ENSP00000443965.2 P55263-1

Frequencies

GnomAD3 genomes
AF:
0.534
AC:
81176
AN:
151918
Hom.:
22725
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.404
Gnomad AMI
AF:
0.497
Gnomad AMR
AF:
0.540
Gnomad ASJ
AF:
0.742
Gnomad EAS
AF:
0.296
Gnomad SAS
AF:
0.427
Gnomad FIN
AF:
0.566
Gnomad MID
AF:
0.631
Gnomad NFE
AF:
0.621
Gnomad OTH
AF:
0.587
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.534
AC:
81188
AN:
152036
Hom.:
22728
Cov.:
32
AF XY:
0.531
AC XY:
39435
AN XY:
74298
show subpopulations
Gnomad4 AFR
AF:
0.403
Gnomad4 AMR
AF:
0.538
Gnomad4 ASJ
AF:
0.742
Gnomad4 EAS
AF:
0.297
Gnomad4 SAS
AF:
0.428
Gnomad4 FIN
AF:
0.566
Gnomad4 NFE
AF:
0.621
Gnomad4 OTH
AF:
0.582
Alfa
AF:
0.613
Hom.:
33993
Bravo
AF:
0.523
Asia WGS
AF:
0.325
AC:
1133
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
6.4
DANN
Benign
0.82

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: rs11000911; hg19: chr10-75946564; API