Genetic Variant ADK:c.555+25404C>T (chr10-74423983-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006721.4(ADK):c.555+25404C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.724 in 161,240 control chromosomes in the GnomAD database, including 42,938 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 0.72 ( 40454 hom., cov: 31)

Exomes 𝑓: 0.72 ( 2484 hom. )

Consequence

ADK
NM_006721.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.95

Publications

3 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 links:

RAB5CP1 (HGNC:45104): (RAB5C, member RAS oncogene family pseudogene 1)

RAB5CP1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADK	NM_006721.4 link	c.555+25404C>T		intron_variant	Intron 6 of 10	ENST00000539909.6	NP_006712.2	P55263-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADK	ENST00000539909.6 link	c.555+25404C>T		intron_variant	Intron 6 of 10	2	NM_006721.4	ENSP00000443965.2		P55263-1

Frequencies

GnomAD3 genomes

AF:

0.724

AC:

109924

AN:

151808

Hom.:

40425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.748

Gnomad AMI

AF:

0.685

Gnomad AMR

AF:

0.701

Gnomad ASJ

AF:

0.868

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.537

Gnomad FIN

AF:

0.663

Gnomad MID

AF:

0.870

Gnomad NFE

AF:

0.752

Gnomad OTH

AF:

0.775

GnomAD4 exome

AF:

0.720

AC:

6712

AN:

9316

Hom.:

2484

Cov.:

AF XY:

0.716

AC XY:

3649

AN XY:

5094

show subpopulations

African (AFR)

AF:

0.793

AC:

119

AN:

150

American (AMR)

AF:

0.661

AC:

152

AN:

230

Ashkenazi Jewish (ASJ)

AF:

0.901

AC:

191

AN:

212

East Asian (EAS)

AF:

0.415

AC:

AN:

212

South Asian (SAS)

AF:

0.596

AC:

929

AN:

1558

European-Finnish (FIN)

AF:

0.692

AC:

480

AN:

694

Middle Eastern (MID)

AF:

0.882

AC:

194

AN:

220

European-Non Finnish (NFE)

AF:

0.757

AC:

4159

AN:

5494

Other (OTH)

AF:

0.733

AC:

400

AN:

546

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.515

Heterozygous variant carriers

175

263

350

438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.724

AC:

110003

AN:

151924

Hom.:

40454

Cov.:

AF XY:

0.716

AC XY:

53187

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.748

AC:

30989

AN:

41438

American (AMR)

AF:

0.700

AC:

10707

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.868

AC:

3011

AN:

3470

East Asian (EAS)

AF:

0.414

AC:

2123

AN:

5128

South Asian (SAS)

AF:

0.539

AC:

2590

AN:

4808

European-Finnish (FIN)

AF:

0.663

AC:

7000

AN:

10558

Middle Eastern (MID)

AF:

0.850

AC:

250

AN:

294

European-Non Finnish (NFE)

AF:

0.752

AC:

51090

AN:

67920

Other (OTH)

AF:

0.769

AC:

1620

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1480

2959

4439

5918

7398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

830

1660

2490

3320

4150

<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:

0.744

Hom.:

6363

Bravo

AF:

0.725

Asia WGS

AF:

0.492

AC:

1713

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

2.0

(source)

DANN

Benign

0.68

PhyloP100

3.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over