rs1379175

Positions:

• chr7-50120593-A-G
• chr7-50120593-A-T

Variant summary

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

The NM_001161834.3(SPATA48):​c.652-9124A>G 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 152,068 control chromosomes in the GnomAD database, including 53,257 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 (53257 hom., cov: 31)
• Consequence: SPATA48 NM_001161834.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA48	NM_001161834.3	c.652-9124A>G		intron_variant		ENST00000297001.7
SPATA48	XM_011515052.2	c.652-9124A>G		intron_variant
SPATA48	XM_011515053.3	c.652-9124A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPMIP7	ENST00000297001.7	c.652-9124A>G		intron_variant		5	NM_001161834.3	P1
ZPBP	ENST00000450231.1	c.-346-197T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127106 AN: 151950 Hom.: 53200 Cov.: 31

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.912

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.837 AC: 127222 AN: 152068 Hom.: 53257 Cov.: 31 AF XY: 0.835 AC XY: 62033 AN XY: 74322

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.840

Gnomad4 OTH AF: 0.816

Alfa AF: 0.836 Hom.: 56830

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	-0.96
CADD	Benign	2.4
DANN	Benign	0.50

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: rs1379175; hg19: chr7-50160189;