2-205184090-G-A

Position:

• chr2-205184090-G-A

Variant summary

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

The NM_001302769.2(PARD3B):​c.1925-1674G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,988 control chromosomes in the GnomAD database, including 3,669 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 0.20 (3669 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.1925-1674G>A		intron_variant		ENST00000406610.7	NP_001289698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARD3B	ENST00000406610.7	c.1925-1674G>A		intron_variant		1	NM_001302769.2	ENSP00000385848	P1
PARD3B	ENST00000349953.7	c.1925-1674G>A		intron_variant		1		ENSP00000340280
PARD3B	ENST00000351153.5	c.1925-1674G>A		intron_variant		1		ENSP00000317261
PARD3B	ENST00000358768.6	c.1739-1674G>A		intron_variant		1		ENSP00000351618

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31149 AN: 151870 Hom.: 3671 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0257

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.205 AC: 31151 AN: 151988 Hom.: 3669 Cov.: 31 AF XY: 0.210 AC XY: 15603 AN XY: 74258

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.0255

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.316

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.215

Alfa AF: 0.244 Hom.: 6338

Bravo AF: 0.187

Asia WGS AF: 0.143 AC: 497 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	1.6
DANN	Benign	0.49

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: rs10170188; hg19: chr2-206048814;