rs1479371

Positions:

• chr3-102299090-C-G

Variant summary

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

The ENST00000491959.5(ZPLD1):​c.-509+69749C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,934 control chromosomes in the GnomAD database, including 8,293 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 0.31 (8293 hom., cov: 32)
• Consequence: ZPLD1 ENST00000491959.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

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]

LOC107986105 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986105	XR_001740817.1	n.75+159C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ZPLD1	ENST00000491959.5	c.-509+69749C>G		intron_variant		1		ENSP00000420265.1

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46559 AN: 151816 Hom.: 8261 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.307 AC: 46626 AN: 151934 Hom.: 8293 Cov.: 32 AF XY: 0.300 AC XY: 22246 AN XY: 74260

Gnomad4 AFR AF: 0.479

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.309

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.290

Alfa AF: 0.265 Hom.: 3108

Bravo AF: 0.314

Asia WGS AF: 0.130 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.099
DANN	Benign	0.32

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: rs1479371; hg19: chr3-102017934;