rs2335704

Variant names:

• chr2-205000109-C-A
• rs2335704
• NM_001302769.2:c.394+34786C>A

Your query was ambiguous. Multiple possible variants found:

• chr2-205000109-C-A
• chr2-205000109-C-G
• chr2-205000109-C-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.394+34786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 151,832 control chromosomes in the GnomAD database, including 57,536 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 0.87 (57536 hom., cov: 29)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 15 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.394+34786C>A		intron_variant	Intron 3 of 22	ENST00000406610.7	NP_001289698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3B	ENST00000406610.7	c.394+34786C>A		intron_variant	Intron 3 of 22	1	NM_001302769.2	ENSP00000385848.2

Frequencies

GnomAD3 genomes AF: 0.870 AC: 131920 AN: 151714 Hom.: 57499 Cov.: 29

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.869 AC: 132015 AN: 151832 Hom.: 57536 Cov.: 29 AF XY: 0.869 AC XY: 64457 AN XY: 74186

African (AFR) AF: 0.809 AC: 33452 AN: 41328

American (AMR) AF: 0.902 AC: 13761 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3015 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5123 AN: 5158

South Asian (SAS) AF: 0.918 AC: 4416 AN: 4812

European-Finnish (FIN) AF: 0.837 AC: 8806 AN: 10518

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60447 AN: 67982

Other (OTH) AF: 0.873 AC: 1842 AN: 2110

Alfa AF: 0.881 Hom.: 67375

Bravo AF: 0.871

Asia WGS AF: 0.950 AC: 3304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.39
PhyloP100		-0.61
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: rs2335704; hg19: chr2-205864832;