Genetic Variant ZPBP2:c.*215A>G (chr17-39877024-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_199321.3(ZPBP2):c.*215A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

ZPBP2
NM_199321.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35

Publications

23 publications found

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]

ZPBP2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZPBP2	NM_199321.3 link	c.*215A>G		3_prime_UTR_variant	Exon 8 of 8	ENST00000348931.9	NP_955353.1	Q6X784-1
ZPBP2	NM_198844.3 link	c.*215A>G		3_prime_UTR_variant	Exon 7 of 7		NP_942141.2	Q6X784-2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ZPBP2	ENST00000348931.9 link	c.*215A>G	3_prime_UTR_variant	Exon 8 of 8	1	NM_199321.3	ENSP00000335384.5	Q6X784-1
ZPBP2	ENST00000377940.3 link	c.*215A>G	3_prime_UTR_variant	Exon 7 of 7	1		ENSP00000367174.3	Q6X784-2
ZPBP2	ENST00000584588.5 link	c.*215A>G	3_prime_UTR_variant	Exon 7 of 7	5		ENSP00000462067.1	J3KRM0
ZPBP2	ENST00000583811.5 link	c.*222A>G	downstream_gene_variant		3		ENSP00000462463.1	J3KSF6

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

293416

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

155092

African (AFR)

AF:

0.00

AC:

AN:

8836

American (AMR)

AF:

0.00

AC:

AN:

13216

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8152

East Asian (EAS)

AF:

0.00

AC:

AN:

18150

South Asian (SAS)

AF:

0.00

AC:

AN:

31432

European-Finnish (FIN)

AF:

0.00

AC:

AN:

15426

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1202

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

180618

Other (OTH)

AF:

0.00

AC:

AN:

16384

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.65

PhyloP100

1.3

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over