7-50107663-C-T

Position:

• chr7-50107663-C-T

Variant summary

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

The NM_001161834.3(SPMIP7):​c.651+3252C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 152,004 control chromosomes in the GnomAD database, including 46,076 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 (46076 hom., cov: 31)
• Consequence: SPMIP7 NM_001161834.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPMIP7	NM_001161834.3	c.651+3252C>T		intron_variant		ENST00000297001.7	NP_001155306.3
SPMIP7	XM_011515052.2	c.651+3252C>T		intron_variant			XP_011513354.1
SPMIP7	XM_011515053.3	c.651+3252C>T		intron_variant			XP_011513355.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA48	ENST00000297001.7	c.651+3252C>T		intron_variant		5	NM_001161834.3	ENSP00000297001.7
ZPBP	ENST00000450231.1	c.10+9590G>A		intron_variant		3		ENSP00000390054.1

Frequencies

GnomAD3 genomes AF: 0.778 AC: 118127 AN: 151886 Hom.: 46050 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.725

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.756

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

GnomAD4 genome AF: 0.778 AC: 118207 AN: 152004 Hom.: 46076 Cov.: 31 AF XY: 0.777 AC XY: 57744 AN XY: 74302

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.733

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.726

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.754

Alfa AF: 0.789 Hom.: 8019

Bravo AF: 0.781

Asia WGS AF: 0.740 AC: 2569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.29
DANN	Benign	0.72

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: rs6972867; hg19: chr7-50147259;