rs10153620

Variant names:

• chr2-205195913-G-C
• rs10153620
• NM_001302769.2:c.2140+2593G>C

Your query was ambiguous. Multiple possible variants found:

• chr2-205195913-G-C
• chr2-205195913-G-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.2140+2593G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 151,724 control chromosomes in the GnomAD database, including 4,943 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 0.25 (4943 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.393
• Publications: 5 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 = 0.328 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.2140+2593G>C		intron	N/A	NP_001289698.1
	PARD3B	NM_152526.6		c.1954+2593G>C		intron	N/A	NP_689739.4
	PARD3B	NM_057177.7		c.2140+2593G>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.2140+2593G>C		intron	N/A	ENSP00000385848.2
	PARD3B	ENST00000358768.6	TSL:1	c.1954+2593G>C		intron	N/A	ENSP00000351618.2
	PARD3B	ENST00000351153.5	TSL:1	c.2140+2593G>C		intron	N/A	ENSP00000317261.2

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37330 AN: 151616 Hom.: 4928 Cov.: 31

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.266

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.246 AC: 37382 AN: 151724 Hom.: 4943 Cov.: 31 AF XY: 0.245 AC XY: 18173 AN XY: 74120

African (AFR) AF: 0.326 AC: 13487 AN: 41372

American (AMR) AF: 0.174 AC: 2647 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 643 AN: 3466

East Asian (EAS) AF: 0.341 AC: 1758 AN: 5152

South Asian (SAS) AF: 0.208 AC: 998 AN: 4796

European-Finnish (FIN) AF: 0.266 AC: 2795 AN: 10492

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14389 AN: 67894

Other (OTH) AF: 0.246 AC: 516 AN: 2100

Alfa AF: 0.131 Hom.: 243

Bravo AF: 0.243

Asia WGS AF: 0.238 AC: 827 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.8
DANN	Benign	0.67
PhyloP100		0.39
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: rs10153620; hg19: chr2-206060637;