dbSNP rs11000897: ADK:c.65+175C>A (chr10-74151518-C-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_006721.4(ADK):c.65+175C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,186 control chromosomes in the GnomAD database, including 1,647 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1647 hom., cov: 32)

Consequence

ADK
NM_006721.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.68

Publications

6 publications found

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]

ADK Gene-Disease associations (from GenCC):

adenosine kinase deficiency
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE, LIMITED Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen

ADK links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 10-74151518-C-A is Benign according to our data. Variant chr10-74151518-C-A is described in ClinVar as Benign. ClinVar VariationId is 1250012.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006721.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADK	NM_006721.4	MANE Select	c.65+175C>A	intron	N/A	NP_006712.2
ADK	NM_001202450.2		c.65+175C>A	intron	N/A	NP_001189379.1	P55263-3
ADK	NM_001369123.1		c.65+175C>A	intron	N/A	NP_001356052.1	A0A5F9ZH31

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ADK	ENST00000539909.6	TSL:2 MANE Select	c.65+175C>A	intron	N/A	ENSP00000443965.2	P55263-1
ADK	ENST00000286621.7	TSL:1	c.65+175C>A	intron	N/A	ENSP00000286621.3	A0A5K1VW54
ADK	ENST00000960305.1		c.65+175C>A	intron	N/A	ENSP00000630364.1

Frequencies

GnomAD3 genomes

AF:

0.144

AC:

21866

AN:

152068

Hom.:

1636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.191

Gnomad AMR

AF:

0.146

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.0981

Gnomad SAS

AF:

0.107

Gnomad FIN

AF:

0.0958

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.132

Gnomad OTH

AF:

0.157

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

GnomAD4 genome

AF:

0.144

AC:

21912

AN:

152186

Hom.:

1647

Cov.:

AF XY:

0.141

AC XY:

10513

AN XY:

74414

show subpopulations

African (AFR)

AF:

0.184

AC:

7623

AN:

41514

American (AMR)

AF:

0.146

AC:

2235

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

455

AN:

3466

East Asian (EAS)

AF:

0.0981

AC:

508

AN:

5176

South Asian (SAS)

AF:

0.108

AC:

524

AN:

4832

European-Finnish (FIN)

AF:

0.0958

AC:

1016

AN:

10606

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.132

AC:

8983

AN:

67994

Other (OTH)

AF:

0.156

AC:

330

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

960

1920

2879

3839

4799

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

238

476

714

952

1190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.133

Hom.:

1714

Bravo

AF:

0.150

Asia WGS

AF:

0.149

AC:

520

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.75

(source)

DANN

Benign

0.63

PhyloP100

-1.7

PromoterAI

-0.020

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over