Genetic Variant NM_174858.3:c.1681_1683dupATT (chr1-77558660-C-CTAT) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_174858.3(AK5):c.1681_1683dupATT(p.Ile561dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.743 in 1,588,160 control chromosomes in the GnomAD database, including 447,473 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.65 ( 34286 hom., cov: 0)

Exomes 𝑓: 0.75 ( 413187 hom. )

Consequence

AK5
NM_174858.3 conservative_inframe_insertion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.19

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_174858.3. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 1-77558660-C-CTAT is Benign according to our data. Variant chr1-77558660-C-CTAT is described in ClinVar as [Benign]. Clinvar id is 402359.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AK5	NM_174858.3 link	c.1681_1683dupATT	p.Ile561dup	conservative_inframe_insertion	Exon 14 of 14	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.1681_1683dupATT	p.Ile561dup	conservative_inframe_insertion	Exon 14 of 14	1	NM_174858.3	ENSP00000346577.2		Q9Y6K8-1

Frequencies

GnomAD3 genomes

AF:

0.652

AC:

98893

AN:

151610

Hom.:

34285

Cov.:

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.682

Gnomad AMR

AF:

0.758

Gnomad ASJ

AF:

0.599

Gnomad EAS

AF:

0.737

Gnomad SAS

AF:

0.657

Gnomad FIN

AF:

0.688

Gnomad MID

AF:

0.623

Gnomad NFE

AF:

0.772

Gnomad OTH

AF:

0.648

GnomAD3 exomes

AF:

0.723

AC:

180057

AN:

249188

Hom.:

66836

AF XY:

0.722

AC XY:

97230

AN XY:

134622

show subpopulations

Gnomad AFR exome

AF:

0.391

Gnomad AMR exome

AF:

0.834

Gnomad ASJ exome

AF:

0.591

Gnomad EAS exome

AF:

0.745

Gnomad SAS exome

AF:

0.661

Gnomad FIN exome

AF:

0.697

Gnomad NFE exome

AF:

0.767

Gnomad OTH exome

AF:

0.700

GnomAD4 exome

AF:

0.753

AC:

1081596

AN:

1436430

Hom.:

413187

Cov.:

AF XY:

0.750

AC XY:

537501

AN XY:

716276

show subpopulations

Gnomad4 AFR exome

AF:

0.387

Gnomad4 AMR exome

AF:

0.825

Gnomad4 ASJ exome

AF:

0.590

Gnomad4 EAS exome

AF:

0.723

Gnomad4 SAS exome

AF:

0.664

Gnomad4 FIN exome

AF:

0.698

Gnomad4 NFE exome

AF:

0.779

Gnomad4 OTH exome

AF:

0.716

GnomAD4 genome

AF:

0.652

AC:

98915

AN:

151730

Hom.:

34286

Cov.:

AF XY:

0.648

AC XY:

48024

AN XY:

74112

show subpopulations

Gnomad4 AFR

AF:

0.399

Gnomad4 AMR

AF:

0.759

Gnomad4 ASJ

AF:

0.599

Gnomad4 EAS

AF:

0.737

Gnomad4 SAS

AF:

0.658

Gnomad4 FIN

AF:

0.688

Gnomad4 NFE

AF:

0.772

Gnomad4 OTH

AF:

0.644

Alfa

AF:

0.685

Hom.:

6248

Bravo

AF:

0.645

Asia WGS

AF:

0.603

AC:

2098

AN:

3478

EpiCase

AF:

0.751

EpiControl

AF:

0.748

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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