rs11886997

Variant names:

• chr2-205466667-C-A
• rs11886997
• NM_001302769.2:c.3044+25995C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302769.2(PARD3B):​c.3044+25995C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,202 control chromosomes in the GnomAD database, including 6,101 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 0.19 (6101 hom., cov: 33)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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.3044+25995C>A		intron	N/A	NP_001289698.1
	PARD3B	NM_152526.6		c.2858+25995C>A		intron	N/A	NP_689739.4
	PARD3B	NM_057177.7		c.2837+25995C>A		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.3044+25995C>A		intron	N/A	ENSP00000385848.2
	PARD3B	ENST00000358768.6	TSL:1	c.2858+25995C>A		intron	N/A	ENSP00000351618.2
	PARD3B	ENST00000351153.5	TSL:1	c.2837+25995C>A		intron	N/A	ENSP00000317261.2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29585 AN: 152084 Hom.: 6070 Cov.: 33

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0891

Gnomad EAS AF: 0.0215

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0463

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.195 AC: 29674 AN: 152202 Hom.: 6101 Cov.: 33 AF XY: 0.187 AC XY: 13952 AN XY: 74424

African (AFR) AF: 0.524 AC: 21732 AN: 41488

American (AMR) AF: 0.117 AC: 1787 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0891 AC: 309 AN: 3468

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5192

South Asian (SAS) AF: 0.0265 AC: 128 AN: 4830

European-Finnish (FIN) AF: 0.0463 AC: 491 AN: 10614

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0679 AC: 4618 AN: 68008

Other (OTH) AF: 0.171 AC: 359 AN: 2104

Alfa AF: 0.0945 Hom.: 2900

Bravo AF: 0.214

Asia WGS AF: 0.0690 AC: 242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.55
PhyloP100		1.1
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: rs11886997; hg19: chr2-206331391;