rs880343

Variant names:

• chr2-205450967-A-G
• rs880343
• NM_001302769.2:c.3044+10295A>G

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+10295A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,268 control chromosomes in the GnomAD database, including 1,252 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 0.11 (1252 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.3044+10295A>G		intron_variant	Intron 20 of 22	ENST00000406610.7	NP_001289698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3B	ENST00000406610.7	c.3044+10295A>G		intron_variant	Intron 20 of 22	1	NM_001302769.2	ENSP00000385848.2
PARD3B	ENST00000358768.6	c.2858+10295A>G		intron_variant	Intron 19 of 21	1		ENSP00000351618.2
PARD3B	ENST00000351153.5	c.2837+10295A>G		intron_variant	Intron 19 of 21	1		ENSP00000317261.2
PARD3B	ENST00000349953.7	c.2742-48929A>G		intron_variant	Intron 19 of 21	1		ENSP00000340280.3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16263 AN: 152150 Hom.: 1249 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0814

Gnomad ASJ AF: 0.0740

Gnomad EAS AF: 0.00885

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.0485

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0679

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.107 AC: 16288 AN: 152268 Hom.: 1252 Cov.: 31 AF XY: 0.102 AC XY: 7604 AN XY: 74466

African (AFR) AF: 0.221 AC: 9165 AN: 41508

American (AMR) AF: 0.0813 AC: 1244 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0740 AC: 257 AN: 3472

East Asian (EAS) AF: 0.00887 AC: 46 AN: 5188

South Asian (SAS) AF: 0.0213 AC: 103 AN: 4832

European-Finnish (FIN) AF: 0.0485 AC: 515 AN: 10622

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0679 AC: 4618 AN: 68022

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0901 Hom.: 180

Bravo AF: 0.115

Asia WGS AF: 0.0340 AC: 117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.34
PhyloP100		0.14
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: rs880343; hg19: chr2-206315691;