rs1296265059

Variant names:

• chr17-45255623-G-A
• rs1296265059
• NM_152343.3:c.559C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-45255623-G-A
• chr17-45255623-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_152343.3(SPATA32):​c.559C>T​(p.Pro187Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P187A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SPATA32 NM_152343.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.039099008).

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.559C>T	p.Pro187Ser	missense	Exon 4 of 5	NP_689556.2	Q96LK8
	MAP3K14-AS1	NR_024434.2		n.79+7620G>A		intron	N/A
	MAP3K14-AS1	NR_110325.1		n.259+405G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA32	ENST00000331780.5	TSL:1 MANE Select	c.559C>T	p.Pro187Ser	missense	Exon 4 of 5	ENSP00000331532.4	Q96LK8
	MAP3K14-AS1	ENST00000590100.7	TSL:1	n.70+7620G>A		intron	N/A
	SPATA32	ENST00000586359.1	TSL:2	n.*1077C>T		non_coding_transcript_exon	Exon 6 of 7	ENSP00000467344.1	K7EPE1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000329 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.089
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.34
DANN	Benign	0.52
DEOGEN2	Benign	0.0048	T
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.017	N
LIST_S2	Benign	0.45	T
M_CAP	Benign	0.0028	T
MetaRNN	Benign	0.039	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.34	N
PhyloP100		-0.60
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.36	N
REVEL	Benign	0.0050
Sift	Benign	0.44	T
Sift4G	Benign	0.49	T
Polyphen		0.078	B
Vest4		0.033
MVP		0.014
MPC		0.19
ClinPred		0.090	T
GERP RS		-3.8
Varity_R		0.021
gMVP		0.054

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: rs1296265059; hg19: chr17-43332990;