2-205609288-T-C

Variant names:

• chr2-205609288-T-C
• rs17626122
• NM_001302769.2:c.3261-6168T>C

Variant summary

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

The NM_001302769.2(PARD3B):​c.3261-6168T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 151,976 control chromosomes in the GnomAD database, including 17,188 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 0.45 (17188 hom., cov: 32)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 3 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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.3261-6168T>C		intron	N/A	NP_001289698.1
	PARD3B	NM_152526.6		c.3075-6168T>C		intron	N/A	NP_689739.4
	PARD3B	NM_057177.7		c.3054-6168T>C		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.3261-6168T>C		intron	N/A	ENSP00000385848.2
	PARD3B	ENST00000358768.6	TSL:1	c.3075-6168T>C		intron	N/A	ENSP00000351618.2
	PARD3B	ENST00000351153.5	TSL:1	c.3054-6168T>C		intron	N/A	ENSP00000317261.2

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68973 AN: 151858 Hom.: 17168 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.454 AC: 69012 AN: 151976 Hom.: 17188 Cov.: 32 AF XY: 0.467 AC XY: 34674 AN XY: 74262

African (AFR) AF: 0.279 AC: 11588 AN: 41472

American (AMR) AF: 0.606 AC: 9255 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1621 AN: 3470

East Asian (EAS) AF: 0.833 AC: 4304 AN: 5166

South Asian (SAS) AF: 0.645 AC: 3098 AN: 4802

European-Finnish (FIN) AF: 0.586 AC: 6181 AN: 10556

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31391 AN: 67932

Other (OTH) AF: 0.444 AC: 938 AN: 2112

Alfa AF: 0.461 Hom.: 28386

Bravo AF: 0.449

Asia WGS AF: 0.732 AC: 2544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.43
PhyloP100		-0.12
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: rs17626122; hg19: chr2-206474012;