2-205396305-G-A

Position:

• chr2-205396305-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.2631-4708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,300 control chromosomes in the GnomAD database, including 59,070 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 0.88 (59070 hom., cov: 34)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3B	NM_001302769.2	c.2631-4708G>A		intron_variant		ENST00000406610.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3B	ENST00000406610.7	c.2631-4708G>A		intron_variant		1	NM_001302769.2	P1

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133517 AN: 152182 Hom.: 59048 Cov.: 34

Gnomad AFR AF: 0.753

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.956

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.877 AC: 133585 AN: 152300 Hom.: 59070 Cov.: 34 AF XY: 0.880 AC XY: 65569 AN XY: 74470

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.934

Gnomad4 FIN AF: 0.956

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.881

Alfa AF: 0.910 Hom.: 26043

Bravo AF: 0.872

Asia WGS AF: 0.939 AC: 3265 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.64

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: rs849230; hg19: chr2-206261029;