Genetic Variant AK5:c.1059+12C>T (chr1-77417727-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_174858.3(AK5):c.1059+12C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,508,818 control chromosomes in the GnomAD database, including 12,933 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.13 ( 1457 hom., cov: 32)

Exomes 𝑓: 0.13 ( 11476 hom. )

Consequence

AK5
NM_174858.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.335

Variant links:

Genes affected

AK5 (HGNC:365): (adenylate kinase 5) This gene encodes a member of the adenylate kinase family, which is involved in regulating the adenine nucleotide composition within a cell by catalyzing the reversible transfer of phosphate groups among adenine nucleotides. This member is related to the UMP/CMP kinase of several species. It is located in the cytosol and expressed exclusively in brain. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

AK5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 1-77417727-C-T is Benign according to our data. Variant chr1-77417727-C-T is described in ClinVar as [Benign]. Clinvar id is 402357.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AK5	NM_174858.3 link	c.1059+12C>T		intron_variant	Intron 8 of 13	ENST00000354567.7	NP_777283.1	Q9Y6K8-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AK5	ENST00000354567.7 link	c.1059+12C>T		intron_variant	Intron 8 of 13	1	NM_174858.3	ENSP00000346577.2		Q9Y6K8-1

Frequencies

GnomAD3 genomes

AF:

0.135

AC:

20510

AN:

152022

Hom.:

1454

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.120

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.131

Gnomad OTH

AF:

0.173

GnomAD3 exomes

AF:

0.135

AC:

32179

AN:

238712

Hom.:

2274

AF XY:

0.136

AC XY:

17543

AN XY:

128692

show subpopulations

Gnomad AFR exome

AF:

0.117

Gnomad AMR exome

AF:

0.140

Gnomad ASJ exome

AF:

0.243

Gnomad EAS exome

AF:

0.121

Gnomad SAS exome

AF:

0.121

Gnomad FIN exome

AF:

0.123

Gnomad NFE exome

AF:

0.134

Gnomad OTH exome

AF:

0.151

GnomAD4 exome

AF:

0.126

AC:

171182

AN:

1356678

Hom.:

11476

Cov.:

AF XY:

0.127

AC XY:

86428

AN XY:

679360

show subpopulations

Gnomad4 AFR exome

AF:

0.120

Gnomad4 AMR exome

AF:

0.142

Gnomad4 ASJ exome

AF:

0.238

Gnomad4 EAS exome

AF:

0.135

Gnomad4 SAS exome

AF:

0.124

Gnomad4 FIN exome

AF:

0.122

Gnomad4 NFE exome

AF:

0.122

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.135

AC:

20530

AN:

152140

Hom.:

1457

Cov.:

AF XY:

0.136

AC XY:

10112

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.169

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.120

Gnomad4 SAS

AF:

0.123

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.175

Alfa

AF:

0.140

Hom.:

372

Bravo

AF:

0.137

Asia WGS

AF:

0.145

AC:

505

AN:

3474

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.75

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over