rs10932110

Variant names:

• chr2-205477169-A-G
• rs10932110
• NM_001302769.2:c.3045-22727A>G

Variant summary

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

The NM_001302769.2(PARD3B):​c.3045-22727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,150 control chromosomes in the GnomAD database, including 5,132 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 0.18 (5132 hom., cov: 32)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.3045-22727A>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.3045-22727A>G		intron_variant	Intron 20 of 22	1	NM_001302769.2	ENSP00000385848.2
PARD3B	ENST00000358768.6	c.2859-22727A>G		intron_variant	Intron 19 of 21	1		ENSP00000351618.2
PARD3B	ENST00000351153.5	c.2838-22727A>G		intron_variant	Intron 19 of 21	1		ENSP00000317261.2
PARD3B	ENST00000349953.7	c.2742-22727A>G		intron_variant	Intron 19 of 21	1		ENSP00000340280.3

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26963 AN: 152032 Hom.: 5102 Cov.: 32

Gnomad AFR AF: 0.480

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.00961

Gnomad SAS AF: 0.0192

Gnomad FIN AF: 0.0436

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.178 AC: 27050 AN: 152150 Hom.: 5132 Cov.: 32 AF XY: 0.171 AC XY: 12695 AN XY: 74388

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.00963

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0436

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.153

Alfa AF: 0.120 Hom.: 482

Bravo AF: 0.196

Asia WGS AF: 0.0550 AC: 192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.27
DANN	Benign	0.28

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: rs10932110; hg19: chr2-206341893;