2-205014778-C-T

Position:

• chr2-205014778-C-T

Variant summary

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

The NM_001302769.2(PARD3B):​c.395-32803C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 151,870 control chromosomes in the GnomAD database, including 10,881 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 0.37 (10881 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3B	NM_001302769.2	c.395-32803C>T		intron_variant		ENST00000406610.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3B	ENST00000406610.7	c.395-32803C>T		intron_variant		1	NM_001302769.2	P1

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56672 AN: 151752 Hom.: 10860 Cov.: 31

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.374 AC: 56739 AN: 151870 Hom.: 10881 Cov.: 31 AF XY: 0.370 AC XY: 27487 AN XY: 74234

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.473

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.242

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.374

Alfa AF: 0.321 Hom.: 1539

Bravo AF: 0.384

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.19

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: rs10172766; hg19: chr2-205879501;