rs8019939

chr14-96397972-A-G

Variant summary

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

The NM_152327.5(AK7):c.106-103A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 1,207,586 control chromosomes in the GnomAD database, including 252,469 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 0.64 (31735 hom., cov: 32)
  • Exomes 𝑓: 0.64 (220734 hom.)
• Consequence: AK7 NM_152327.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

Genes affected

AK7 (HGNC:20091): (adenylate kinase 7) This gene encodes a member of the adenylate kinase family of enzymes. The encoded enzyme is a phosphotransferase that catalyzes the reversible phosphorylation of adenine nucleotides. This enzyme plays a role in energy homeostasis of the cell. Alternative splicing results in multiple transcript variants. Mutations in the mouse gene are associated with primary ciliary dyskinesia. [provided by RefSeq, Apr 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AK7	NM_152327.5	c.106-103A>G		intron_variant		ENST00000267584.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AK7	ENST00000267584.9	c.106-103A>G		intron_variant		1	NM_152327.5	P1
AK7	ENST00000555570.1	c.106-103A>G		intron_variant		2
AK7	ENST00000556643.1	n.117-103A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97910 AN: 151936 Hom.: 31709 Cov.: 32

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.664

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.638

GnomAD4 exome AF: 0.645 AC: 680305 AN: 1055532 Hom.: 220734 AF XY: 0.645 AC XY: 343599 AN XY: 533106

Gnomad4 AFR exome AF: 0.655

Gnomad4 AMR exome AF: 0.549

Gnomad4 ASJ exome AF: 0.659

Gnomad4 EAS exome AF: 0.843

Gnomad4 SAS exome AF: 0.653

Gnomad4 FIN exome AF: 0.624

Gnomad4 NFE exome AF: 0.639

Gnomad4 OTH exome AF: 0.643

GnomAD4 genome AF: 0.644 AC: 97996 AN: 152054 Hom.: 31735 Cov.: 32 AF XY: 0.645 AC XY: 47946 AN XY: 74322

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.664

Gnomad4 EAS AF: 0.830

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.640

Alfa AF: 0.636 Hom.: 41802

Bravo AF: 0.642

Asia WGS AF: 0.729 AC: 2538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.20
Dann	Benign	0.29

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs8019939; hg19: chr14-96864309;