2-205069931-G-A

Variant names:

• chr2-205069931-G-A
• rs1510772
• NM_001302769.2:c.504+22241G>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.504+22241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 152,060 control chromosomes in the GnomAD database, including 5,899 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 0.27 (5899 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.443
• Publications: 5 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]

ENSG00000309354 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.447 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.504+22241G>A		intron	N/A	NP_001289698.1
	PARD3B	NM_152526.6		c.504+22241G>A		intron	N/A	NP_689739.4
	PARD3B	NM_057177.7		c.504+22241G>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.504+22241G>A		intron	N/A	ENSP00000385848.2
	PARD3B	ENST00000358768.6	TSL:1	c.504+22241G>A		intron	N/A	ENSP00000351618.2
	PARD3B	ENST00000351153.5	TSL:1	c.504+22241G>A		intron	N/A	ENSP00000317261.2

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40400 AN: 151942 Hom.: 5904 Cov.: 31

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.266 AC: 40394 AN: 152060 Hom.: 5899 Cov.: 31 AF XY: 0.272 AC XY: 20195 AN XY: 74308

African (AFR) AF: 0.185 AC: 7694 AN: 41508

American (AMR) AF: 0.215 AC: 3282 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3470

East Asian (EAS) AF: 0.425 AC: 2190 AN: 5154

South Asian (SAS) AF: 0.463 AC: 2226 AN: 4812

European-Finnish (FIN) AF: 0.328 AC: 3461 AN: 10556

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.287 AC: 19483 AN: 67982

Other (OTH) AF: 0.262 AC: 551 AN: 2106

Alfa AF: 0.255 Hom.: 891

Bravo AF: 0.252

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.31
PhyloP100		0.44
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: rs1510772; hg19: chr2-205934654;