rs1510772

chr2-205069931-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.504+22241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,060 control chromosomes in the GnomAD database, including 5,899 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 0.27 (5899 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3B	NM_001302769.2	c.504+22241G>A		intron_variant		ENST00000406610.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3B	ENST00000406610.7	c.504+22241G>A		intron_variant		1	NM_001302769.2	P1
PARD3B	ENST00000349953.7	c.504+22241G>A		intron_variant		1
PARD3B	ENST00000351153.5	c.504+22241G>A		intron_variant		1
PARD3B	ENST00000358768.6	c.504+22241G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40400 AN: 151942 Hom.: 5904 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.266 AC: 40394 AN: 152060 Hom.: 5899 Cov.: 31 AF XY: 0.272 AC XY: 20195 AN XY: 74308

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.262

Alfa AF: 0.255 Hom.: 891

Bravo AF: 0.252

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2
Dann	Benign	0.31

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: rs1510772; hg19: chr2-205934654;