17-45261574-G-C

Variant names:

• chr17-45261574-G-C
• rs7215764
• NM_152343.3:c.13+430C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152343.3(SPATA32):​c.13+430C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,202 control chromosomes in the GnomAD database, including 47,007 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (47007 hom., cov: 32)
• Consequence: SPATA32 NM_152343.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 7 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA32	NM_152343.3	c.13+430C>G		intron_variant	Intron 1 of 4	ENST00000331780.5	NP_689556.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA32	ENST00000331780.5	c.13+430C>G		intron_variant	Intron 1 of 4	1	NM_152343.3	ENSP00000331532.4

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118771 AN: 152084 Hom.: 46959 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.781 AC: 118872 AN: 152202 Hom.: 47007 Cov.: 32 AF XY: 0.776 AC XY: 57717 AN XY: 74386

African (AFR) AF: 0.904 AC: 37579 AN: 41562

American (AMR) AF: 0.780 AC: 11936 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2420 AN: 3468

East Asian (EAS) AF: 0.735 AC: 3801 AN: 5170

South Asian (SAS) AF: 0.650 AC: 3135 AN: 4822

European-Finnish (FIN) AF: 0.699 AC: 7389 AN: 10568

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.738 AC: 50181 AN: 67998

Other (OTH) AF: 0.744 AC: 1572 AN: 2114

Alfa AF: 0.768 Hom.: 5586

Bravo AF: 0.791

Asia WGS AF: 0.708 AC: 2462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.061
DANN	Benign	0.36
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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: rs7215764; hg19: chr17-43338941;