rs13410658

chr2-205477358-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.3045-22538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,084 control chromosomes in the GnomAD database, including 2,753 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 0.14 (2753 hom., cov: 32)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445

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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3B	NM_001302769.2	c.3045-22538C>T		intron_variant		ENST00000406610.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3B	ENST00000406610.7	c.3045-22538C>T		intron_variant		1	NM_001302769.2	P1
PARD3B	ENST00000349953.7	c.2742-22538C>T		intron_variant		1
PARD3B	ENST00000351153.5	c.2838-22538C>T		intron_variant		1
PARD3B	ENST00000358768.6	c.2859-22538C>T		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21087 AN: 151966 Hom.: 2737 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.00962

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.139 AC: 21152 AN: 152084 Hom.: 2753 Cov.: 32 AF XY: 0.134 AC XY: 9946 AN XY: 74354

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.0949

Gnomad4 ASJ AF: 0.0806

Gnomad4 EAS AF: 0.00964

Gnomad4 SAS AF: 0.0191

Gnomad4 FIN AF: 0.0439

Gnomad4 NFE AF: 0.0599

Gnomad4 OTH AF: 0.123

Alfa AF: 0.0617 Hom.: 243

Bravo AF: 0.152

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	14
Dann	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs13410658; hg19: chr2-206342082;