17-32996938-AGC-CGA

Variant names:

• chr17-32996938-AGC-CGA
• NM_173847.5:c.439_441delAGCinsCGA
• SPACA3 p.Ser147Arg

Variant summary

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

The NM_173847.5(SPACA3):​c.439_441delAGCinsCGA​(p.Ser147Arg) variant causes a missense 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SPACA3 NM_173847.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.47
• Publications: 0 publications found

Genes affected

SPACA3 (HGNC:16260): (sperm acrosome associated 3) The protein encoded by this gene is a sperm surface protein that may be involved in adhesion to the egg prior to fertilization. While the encoded protein has significant similarity to lysozyme at the amino acid level, it has no detectable bacteriocidal activity. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2015]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173847.5. 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
	SPACA3	NM_173847.5	MANE Select	c.439_441delAGCinsCGA	p.Ser147Arg	missense	N/A	NP_776246.1	Q8IXA5-1
	SPACA3	NM_001317225.2		c.163_165delAGCinsCGA	p.Ser55Arg	missense	N/A	NP_001304154.1	Q05C28
	SPACA3	NM_001317226.2		c.130_132delAGCinsCGA	p.Ser44Arg	missense	N/A	NP_001304155.1	E9PF91

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPACA3	ENST00000269053.8	TSL:1 MANE Select	c.439_441delAGCinsCGA	p.Ser147Arg	missense	N/A	ENSP00000269053.3	Q8IXA5-1
	SPACA3	ENST00000580599.5	TSL:1	c.232_234delAGCinsCGA	p.Ser78Arg	missense	N/A	ENSP00000463386.1	Q8IXA5-2
	SPACA3	ENST00000394637.2	TSL:1	n.582_584delAGCinsCGA		non_coding_transcript_exon	Exon 3 of 5

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.5

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: chr17-31323956;