17-45255756-CAC-GAG

Variant names:

• chr17-45255756-CAC-GAG
• NM_152343.3:c.424_426delGTGinsCTC
• SPATA32 p.Val142Leu

Variant summary

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

The NM_152343.3(SPATA32):​c.424_426delGTGinsCTC​(p.Val142Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 31)
• Consequence: SPATA32 NM_152343.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292
• Publications: 0 publications found

Genes affected

SPATA32 (HGNC:26349): (spermatogenesis associated 32) Predicted to enable actin binding activity. Predicted to be involved in spermatogenesis. Predicted to be active in perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

MAP3K14-AS1 (HGNC:44359): (MAP3K14 antisense RNA 1)

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152343.3. 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
	SPATA32	NM_152343.3	MANE Select	c.424_426delGTGinsCTC	p.Val142Leu	missense	N/A	NP_689556.2	Q96LK8
	MAP3K14-AS1	NR_024434.2		n.79+7753_79+7755delCACinsGAG		intron	N/A
	MAP3K14-AS1	NR_110325.1		n.259+538_259+540delCACinsGAG		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA32	ENST00000331780.5	TSL:1 MANE Select	c.424_426delGTGinsCTC	p.Val142Leu	missense	N/A	ENSP00000331532.4	Q96LK8
	MAP3K14-AS1	ENST00000590100.7	TSL:1	n.70+7753_70+7755delCACinsGAG		intron	N/A
	SPATA32	ENST00000586359.1	TSL:2	n.*942_*944delGTGinsCTC		non_coding_transcript_exon	Exon 6 of 7	ENSP00000467344.1	K7EPE1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.29

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: chr17-43333123;