chr2-205425652-A-G

Variant names:

• chr2-205425652-A-G
• rs10210768
• NM_001302769.2:c.2742-14718A>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.2742-14718A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,154 control chromosomes in the GnomAD database, including 1,340 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 (1340 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.2742-14718A>G		intron_variant	Intron 19 of 22	ENST00000406610.7	NP_001289698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3B	ENST00000406610.7	c.2742-14718A>G		intron_variant	Intron 19 of 22	1	NM_001302769.2	ENSP00000385848.2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16787 AN: 152038 Hom.: 1337 Cov.: 31

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0769

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0212

Gnomad FIN AF: 0.0481

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0731

Gnomad OTH AF: 0.0999

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

GnomAD4 genome AF: 0.111 AC: 16817 AN: 152154 Hom.: 1340 Cov.: 31 AF XY: 0.105 AC XY: 7814 AN XY: 74384

African (AFR) AF: 0.227 AC: 9428 AN: 41492

American (AMR) AF: 0.0768 AC: 1173 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0769 AC: 267 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5172

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4816

European-Finnish (FIN) AF: 0.0481 AC: 510 AN: 10600

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

European-Non Finnish (NFE) AF: 0.0730 AC: 4968 AN: 68014

Other (OTH) AF: 0.0989 AC: 209 AN: 2114

Alfa AF: 0.0937 Hom.: 247

Bravo AF: 0.118

Asia WGS AF: 0.0310 AC: 106 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.5
DANN	Benign	0.72
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: rs10210768; hg19: chr2-206290376;