rs10212363

Positions:

• chr3-102129717-G-A

Variant summary

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

The ENST00000491959.5(ZPLD1):​c.-779+28146G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,030 control chromosomes in the GnomAD database, including 3,266 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 0.21 (3266 hom., cov: 32)
• Consequence: ZPLD1 ENST00000491959.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

ZPLD1 (HGNC:27022): (zona pellucida like domain containing 1) Predicted to be an extracellular matrix structural constituent. Predicted to act upstream of or within vestibular reflex. Predicted to be located in cytoplasmic vesicle membrane. Predicted to be integral component of membrane. Predicted to be active in cell surface and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZPLD1	ENST00000491959.5	c.-779+28146G>A		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31322 AN: 151912 Hom.: 3262 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.206 AC: 31344 AN: 152030 Hom.: 3266 Cov.: 32 AF XY: 0.204 AC XY: 15130 AN XY: 74304

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.212

Alfa AF: 0.211 Hom.: 525

Bravo AF: 0.207

Asia WGS AF: 0.167 AC: 582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.90
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: rs10212363; hg19: chr3-101848561;