rs587777029

Variant names:

• chr14-96456418-C-CT
• rs587777029
• NM_152327.5:c.1171dupT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_152327.5(AK7):​c.1171dupT​(p.Tyr391LeufsTer14) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AK7 NM_152327.5 frameshift
• Clinical Significance: Uncertain significance no assertion criteria provided U:1
• Conservation: PhyloP100: 6.60
• Publications: 0 publications found

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]

RPL23AP10 (HGNC:19804): (ribosomal protein L23a pseudogene 10)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152327.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AK7	NM_152327.5	MANE Select	c.1171dupT	p.Tyr391LeufsTer14	frameshift	Exon 11 of 18	NP_689540.2	Q96M32
	AK7	NM_001350888.2		c.1171dupT	p.Tyr391LeufsTer14	frameshift	Exon 11 of 17	NP_001337817.1
	AK7	NM_001350890.2		c.1171dupT	p.Tyr391LeufsTer14	frameshift	Exon 11 of 17	NP_001337819.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AK7	ENST00000267584.9	TSL:1 MANE Select	c.1171dupT	p.Tyr391LeufsTer14	frameshift	Exon 11 of 18	ENSP00000267584.4	Q96M32
	AK7	ENST00000856706.1		c.1255dupT	p.Tyr419LeufsTer14	frameshift	Exon 12 of 19	ENSP00000526765.1
	AK7	ENST00000856705.1		c.1171dupT	p.Tyr391LeufsTer14	frameshift	Exon 11 of 17	ENSP00000526764.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	1	-	Primary ciliary dyskinesia (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.6

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs587777029;

hg19: chr14-96922755;