rs12936231

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000348931.9(ZPBP2):​c.626-177C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,030 control chromosomes in the GnomAD database, including 19,088 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 0.50 ( 19088 hom., cov: 32)

Consequence

ZPBP2
ENST00000348931.9 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.11
Variant links:
Genes affected
ZPBP2 (HGNC:20678): (zona pellucida binding protein 2) Predicted to be involved in acrosome assembly and binding activity of sperm to zona pellucida. Predicted to act upstream of or within membrane lipid metabolic process and regulation of gene expression. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZPBP2NM_199321.3 linkuse as main transcriptc.626-177C>G intron_variant ENST00000348931.9 NP_955353.1
ZPBP2NM_198844.3 linkuse as main transcriptc.560-177C>G intron_variant NP_942141.2
ZPBP2XM_047435318.1 linkuse as main transcriptc.626-177C>G intron_variant XP_047291274.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZPBP2ENST00000348931.9 linkuse as main transcriptc.626-177C>G intron_variant 1 NM_199321.3 ENSP00000335384 P1Q6X784-1
ZPBP2ENST00000377940.3 linkuse as main transcriptc.560-177C>G intron_variant 1 ENSP00000367174 Q6X784-2
ZPBP2ENST00000583811.5 linkuse as main transcriptc.272-177C>G intron_variant 3 ENSP00000462463
ZPBP2ENST00000584588.5 linkuse as main transcriptc.407-177C>G intron_variant 5 ENSP00000462067

Frequencies

GnomAD3 genomes
AF:
0.498
AC:
75631
AN:
151912
Hom.:
19042
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.540
Gnomad AMI
AF:
0.670
Gnomad AMR
AF:
0.445
Gnomad ASJ
AF:
0.463
Gnomad EAS
AF:
0.271
Gnomad SAS
AF:
0.396
Gnomad FIN
AF:
0.575
Gnomad MID
AF:
0.456
Gnomad NFE
AF:
0.497
Gnomad OTH
AF:
0.478
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.498
AC:
75744
AN:
152030
Hom.:
19088
Cov.:
32
AF XY:
0.497
AC XY:
36949
AN XY:
74290
show subpopulations
Gnomad4 AFR
AF:
0.541
Gnomad4 AMR
AF:
0.446
Gnomad4 ASJ
AF:
0.463
Gnomad4 EAS
AF:
0.271
Gnomad4 SAS
AF:
0.396
Gnomad4 FIN
AF:
0.575
Gnomad4 NFE
AF:
0.497
Gnomad4 OTH
AF:
0.476
Alfa
AF:
0.479
Hom.:
2080
Bravo
AF:
0.484
Asia WGS
AF:
0.418
AC:
1454
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.41
CADD
Benign
19
DANN
Benign
0.86

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs12936231; hg19: chr17-38029120; API