14-96404767-G-A

Position:

• chr14-96404767-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_152327.5(AK7):​c.305G>A​(p.Arg102Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 1,597,578 control chromosomes in the GnomAD database, including 46,816 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

• Frequency:
  • Genomes: 𝑓 0.23 (4097 hom., cov: 32)
  • Exomes 𝑓: 0.24 (42719 hom.)
• Consequence: AK7 NM_152327.5 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: 2.47

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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0016051829).
• BP6: Variant 14-96404767-G-A is Benign according to our data. Variant chr14-96404767-G-A is described in ClinVar as [Benign]. Clinvar id is 402360.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AK7	NM_152327.5	c.305G>A	p.Arg102Gln	missense_variant	3/18	ENST00000267584.9	NP_689540.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AK7	ENST00000267584.9	c.305G>A	p.Arg102Gln	missense_variant	3/18	1	NM_152327.5	ENSP00000267584	P1
AK7	ENST00000554313.1	n.77G>A		non_coding_transcript_exon_variant	2/5	3
AK7	ENST00000556643.1	n.316G>A		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.231 AC: 35017 AN: 151846 Hom.: 4097 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.234

GnomAD3 exomes AF: 0.219 AC: 55020 AN: 251018 Hom.: 6247 AF XY: 0.221 AC XY: 30001 AN XY: 135660

Gnomad AFR exome AF: 0.220

Gnomad AMR exome AF: 0.164

Gnomad ASJ exome AF: 0.321

Gnomad EAS exome AF: 0.187

Gnomad SAS exome AF: 0.179

Gnomad FIN exome AF: 0.191

Gnomad NFE exome AF: 0.247

Gnomad OTH exome AF: 0.245

GnomAD4 exome AF: 0.240 AC: 346720 AN: 1445612 Hom.: 42719 Cov.: 30 AF XY: 0.238 AC XY: 170960 AN XY: 717060

Gnomad4 AFR exome AF: 0.211

Gnomad4 AMR exome AF: 0.170

Gnomad4 ASJ exome AF: 0.324

Gnomad4 EAS exome AF: 0.201

Gnomad4 SAS exome AF: 0.178

Gnomad4 FIN exome AF: 0.198

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.242

GnomAD4 genome AF: 0.231 AC: 35039 AN: 151966 Hom.: 4097 Cov.: 32 AF XY: 0.227 AC XY: 16844 AN XY: 74264

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.237

Alfa AF: 0.248 Hom.: 9090

Bravo AF: 0.232

TwinsUK AF: 0.239 AC: 885

ALSPAC AF: 0.252 AC: 972

ESP6500AA AF: 0.229 AC: 1009

ESP6500EA AF: 0.255 AC: 2191

ExAC AF: 0.218 AC: 26487

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -

not specified Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.61	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	21
DANN	Benign	0.96
DEOGEN2	Benign	0.12	T
Eigen	Benign	-0.42
Eigen_PC	Benign	-0.35
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.81	T
MetaRNN	Benign	0.0016	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.8	L
MutationTaster	Benign	0.0073	P
PrimateAI	Benign	0.31	T
PROVEAN	Benign	-1.9	N
REVEL	Benign	0.026
Sift	Benign	0.15	T
Sift4G	Benign	0.16	T
Polyphen		0.15	B
Vest4		0.055
MPC		0.23
ClinPred		0.010	T
GERP RS		4.5
Varity_R		0.11
gMVP		0.50

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: rs2275554; hg19: chr14-96871104; COSMIC: COSV50871708;