rs1871084

chr10-74423983-C-T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.95

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]

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ADK	NM_006721.4	c.555+25404C>T		intron_variant		ENST00000539909.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADK	ENST00000539909.6	c.555+25404C>T		intron_variant		2	NM_006721.4	P3
RAB5CP1	ENST00000395972.2	n.32G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109924 AN: 151808 Hom.: 40425 Cov.: 31

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.: 0 AF XY: 0.716 AC XY: 3649 AN XY: 5094

Gnomad4 AFR exome AF: 0.793

Gnomad4 AMR exome AF: 0.661

Gnomad4 ASJ exome AF: 0.901

Gnomad4 EAS exome AF: 0.415

Gnomad4 SAS exome AF: 0.596

Gnomad4 FIN exome AF: 0.692

Gnomad4 NFE exome AF: 0.757

Gnomad4 OTH exome AF: 0.733

GnomAD4 genome AF: 0.724 AC: 110003 AN: 151924 Hom.: 40454 Cov.: 31 AF XY: 0.716 AC XY: 53187 AN XY: 74234

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.769

Alfa AF: 0.743 Hom.: 6124

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
Dann	Benign	0.68

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: rs1871084; hg19: chr10-76183741;