rs10153620

chr2-205195913-G-Cchr2-205195913-G-T

Variant summary

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

The NM_001302769.2(PARD3B):c.2140+2593G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,724 control chromosomes in the GnomAD database, including 4,943 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 0.25 (4943 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3B	NM_001302769.2	c.2140+2593G>C		intron_variant		ENST00000406610.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3B	ENST00000406610.7	c.2140+2593G>C		intron_variant		1	NM_001302769.2	P1
PARD3B	ENST00000349953.7	c.2140+2593G>C		intron_variant		1
PARD3B	ENST00000351153.5	c.2140+2593G>C		intron_variant		1
PARD3B	ENST00000358768.6	c.1954+2593G>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37330 AN: 151616 Hom.: 4928 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.246 AC: 37382 AN: 151724 Hom.: 4943 Cov.: 31 AF XY: 0.245 AC XY: 18173 AN XY: 74120

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.341

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.266

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.246

Alfa AF: 0.131 Hom.: 243

Bravo AF: 0.243

Asia WGS AF: 0.238 AC: 827 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.8
Dann	Benign	0.67

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: rs10153620; hg19: chr2-206060637;