rs1037675

chr7-50119761-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001161834.3(SPATA48):c.652-9956G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 152,180 control chromosomes in the GnomAD database, including 53,293 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 0.84 (53293 hom., cov: 33)
• Consequence: SPATA48 NM_001161834.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.612

Genes affected

SPATA48 (HGNC:):

SPMIP7 (HGNC:22564): (sperm microtubule inner protein 7)

ZPBP (HGNC:15662): (zona pellucida binding protein) ZPBP is one of several proteins that are thought to participate in secondary binding between acrosome-reacted sperm and the egg-specific extracellular matrix, the zona pellucida (McLeskey et al., 1998 [PubMed 9378618]).[supplied by OMIM, Aug 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA48	NM_001161834.3	c.652-9956G>A		intron_variant		ENST00000297001.7
SPATA48	XM_011515052.2	c.652-9956G>A		intron_variant
SPATA48	XM_011515053.3	c.652-9956G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPMIP7	ENST00000297001.7	c.652-9956G>A		intron_variant		5	NM_001161834.3	P1
ZPBP	ENST00000450231.1	c.-158+447C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127188 AN: 152062 Hom.: 53236 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.837 AC: 127304 AN: 152180 Hom.: 53293 Cov.: 33 AF XY: 0.835 AC XY: 62101 AN XY: 74412

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.816

Alfa AF: 0.835 Hom.: 6582

Bravo AF: 0.841

Asia WGS AF: 0.865 AC: 3006 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.72
Dann	Benign	0.22

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037675; hg19: chr7-50159357;