2-205014778-C-T

Variant names:

• chr2-205014778-C-T
• rs10172766
• NM_001302769.2:c.395-32803C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302769.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3B	NM_001302769.2	MANE Select	c.395-32803C>T		intron	N/A	NP_001289698.1
	PARD3B	NM_152526.6		c.395-32803C>T		intron	N/A	NP_689739.4
	PARD3B	NM_057177.7		c.395-32803C>T		intron	N/A	NP_476518.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3B	ENST00000406610.7	TSL:1 MANE Select	c.395-32803C>T		intron	N/A	ENSP00000385848.2
	PARD3B	ENST00000358768.6	TSL:1	c.395-32803C>T		intron	N/A	ENSP00000351618.2
	PARD3B	ENST00000351153.5	TSL:1	c.395-32803C>T		intron	N/A	ENSP00000317261.2

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

African (AFR) AF: 0.364 AC: 15071 AN: 41368

American (AMR) AF: 0.473 AC: 7223 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.425 AC: 1470 AN: 3462

East Asian (EAS) AF: 0.165 AC: 853 AN: 5160

South Asian (SAS) AF: 0.242 AC: 1165 AN: 4814

European-Finnish (FIN) AF: 0.357 AC: 3766 AN: 10546

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25941 AN: 67942

Other (OTH) AF: 0.374 AC: 788 AN: 2106

Alfa AF: 0.343 Hom.: 3204

Bravo AF: 0.384

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.19
PhyloP100		0.19
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10172766; hg19: chr2-205879501;