rs6485

Variant names:

• chr1-77558660-CTAT-C
• rs6485
• NM_174858.3:c.1681_1683delATT

Your query was ambiguous. Multiple possible variants found:

• chr1-77558660-CTAT-C
• chr1-77558660-CTAT-CTATTATAT
• chr1-77558660-CTAT-CTATTAT
• chr1-77558660-CTAT-CTATTATTAT

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PM4_Supporting

The NM_174858.3(AK5):​c.1681_1683delATT​(p.Ile561del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: AK5 NM_174858.3 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.85
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_174858.3. Strenght limited to Supporting due to length of the change: 1aa.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174858.3. 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
	AK5	NM_174858.3	MANE Select	c.1681_1683delATT	p.Ile561del	conservative_inframe_deletion	Exon 14 of 14	NP_777283.1	Q9Y6K8-1
	AK5	NM_012093.4		c.1603_1605delATT	p.Ile535del	conservative_inframe_deletion	Exon 14 of 14	NP_036225.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AK5	ENST00000354567.7	TSL:1 MANE Select	c.1681_1683delATT	p.Ile561del	conservative_inframe_deletion	Exon 14 of 14	ENSP00000346577.2	Q9Y6K8-1
	AK5	ENST00000344720.9	TSL:1	c.1603_1605delATT	p.Ile535del	conservative_inframe_deletion	Exon 14 of 14	ENSP00000341430.5	Q9Y6K8-3
	AK5	ENST00000478255.1	TSL:2	c.226_228delATT	p.Ile76del	conservative_inframe_deletion	Exon 3 of 3	ENSP00000433915.1	E9PIS7

Frequencies

GnomAD3 genomes Cov.: 0

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.9

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

Other links and lift over

dbSNP: rs6485; hg19: chr1-78024345;