rs1207421

Positions:

• chr2-205285870-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302769.2(PARD3B):​c.2186-14660A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,190 control chromosomes in the GnomAD database, including 62,633 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 0.91 (62633 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.2186-14660A>G		intron_variant		ENST00000406610.7	NP_001289698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARD3B	ENST00000406610.7	c.2186-14660A>G		intron_variant		1	NM_001302769.2	ENSP00000385848.2
PARD3B	ENST00000358768.6	c.2000-14660A>G		intron_variant		1		ENSP00000351618.2
PARD3B	ENST00000351153.5	c.2186-15594A>G		intron_variant		1		ENSP00000317261.2
PARD3B	ENST00000349953.7	c.2186-14660A>G		intron_variant		1		ENSP00000340280.3

Frequencies

GnomAD3 genomes AF: 0.906 AC: 137752 AN: 152072 Hom.: 62575 Cov.: 31

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.917

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.906 AC: 137867 AN: 152190 Hom.: 62633 Cov.: 31 AF XY: 0.907 AC XY: 67513 AN XY: 74402

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.942

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.912

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.906

Alfa AF: 0.899 Hom.: 131114

Bravo AF: 0.907

Asia WGS AF: 0.841 AC: 2924 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.50

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

Publications

LitVar

Other links and lift over

dbSNP: rs1207421; hg19: chr2-206150594;