chr7-50053482-C-G

Position:

• chr7-50053482-C-G

Variant summary

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

The ENST00000046087.7(ZPBP):​c.487+4507G>C variant causes a intron change. The variant allele was found at a frequency of 0.768 in 152,110 control chromosomes in the GnomAD database, including 44,959 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 0.77 (44959 hom., cov: 34)
• Consequence: ZPBP ENST00000046087.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.84

Genes affected

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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ZPBP	NM_007009.3	c.487+4507G>C		intron_variant		ENST00000046087.7	NP_008940.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZPBP	ENST00000046087.7	c.487+4507G>C		intron_variant		1	NM_007009.3	ENSP00000046087	P4
ZPBP	ENST00000419417.5	c.484+4507G>C		intron_variant		1		ENSP00000402071	A2
ZPBP	ENST00000491129.5	n.240+2703G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.768 AC: 116685 AN: 151992 Hom.: 44922 Cov.: 34

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.768 AC: 116780 AN: 152110 Hom.: 44959 Cov.: 34 AF XY: 0.765 AC XY: 56857 AN XY: 74356

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.711

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.777

Gnomad4 OTH AF: 0.740

Alfa AF: 0.707 Hom.: 2096

Bravo AF: 0.762

Asia WGS AF: 0.739 AC: 2564 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.54

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: rs1355037; hg19: chr7-50093078;