9-4662562-AGC-TCT

Variant names:

• chr9-4662562-AGC-TCT
• NM_203453.5:c.187_189delAGCinsTCT
• PLPP6 p.64

Variant summary

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

The NM_203453.5(PLPP6):​c.187_189delAGCinsTCT​(p.64) variant causes a synonymous change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PLPP6 NM_203453.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.60
• Publications: 0 publications found

Genes affected

PLPP6 (HGNC:23682): (phospholipid phosphatase 6) Enables lipid phosphatase activity. Involved in phospholipid dephosphorylation. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in sperm connecting piece. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_203453.5. 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
	PLPP6	NM_203453.5	MANE Select	c.187_189delAGCinsTCT	p.64	synonymous	N/A	NP_982278.3	Q8IY26
	SPATA6L	NM_001353486.2	MANE Select	c.40-528_40-526delGCTinsAGA		intron	N/A	NP_001340415.1	Q8N4H0-1
	SPATA6L	NM_001353484.2		c.40-528_40-526delGCTinsAGA		intron	N/A	NP_001340413.1	A0AA34QVF8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLPP6	ENST00000381883.5	TSL:6 MANE Select	c.187_189delAGCinsTCT	p.64	synonymous	N/A	ENSP00000371307.2	Q8IY26
	SPATA6L	ENST00000682582.1	MANE Select	c.40-528_40-526delGCTinsAGA		intron	N/A	ENSP00000506787.1	Q8N4H0-1
	SPATA6L	ENST00000451763.6	TSL:1	n.189-528_189-526delGCTinsAGA		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		6.6

Splicing

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

hg19: chr9-4662562;