rs11886997

chr2-205466667-C-A

Variant summary

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

The NM_001302769.2(PARD3B):c.3044+25995C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,202 control chromosomes in the GnomAD database, including 6,101 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 0.19 (6101 hom., cov: 33)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

PARD3B (HGNC:14446): (par-3 family cell polarity regulator beta) Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in several processes, including establishment of cell polarity; establishment of centrosome localization; and establishment or maintenance of epithelial cell apical/basal polarity. Located in cell junction. Part of protein-containing complex. [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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3B	NM_001302769.2	c.3044+25995C>A		intron_variant		ENST00000406610.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3B	ENST00000406610.7	c.3044+25995C>A		intron_variant		1	NM_001302769.2	P1
PARD3B	ENST00000349953.7	c.2742-33229C>A		intron_variant		1
PARD3B	ENST00000351153.5	c.2837+25995C>A		intron_variant		1
PARD3B	ENST00000358768.6	c.2858+25995C>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29585 AN: 152084 Hom.: 6070 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.195 AC: 29674 AN: 152202 Hom.: 6101 Cov.: 33 AF XY: 0.187 AC XY: 13952 AN XY: 74424

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0891

Gnomad4 EAS AF: 0.0216

Gnomad4 SAS AF: 0.0265

Gnomad4 FIN AF: 0.0463

Gnomad4 NFE AF: 0.0679

Gnomad4 OTH AF: 0.171

Alfa AF: 0.119 Hom.: 942

Bravo AF: 0.214

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.5
Dann	Benign	0.55

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: rs11886997; hg19: chr2-206331391;