rs13410658

Variant names:

• chr2-205477358-C-T
• rs13410658
• NM_001302769.2:c.3045-22538C>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.3045-22538C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,084 control chromosomes in the GnomAD database, including 2,753 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 0.14 (2753 hom., cov: 32)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 1 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=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.342 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3B	NM_001302769.2	MANE Select	c.3045-22538C>T		intron	N/A	NP_001289698.1	Q8TEW8-1
	PARD3B	NM_152526.6		c.2859-22538C>T		intron	N/A	NP_689739.4
	PARD3B	NM_057177.7		c.2838-22538C>T		intron	N/A	NP_476518.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3B	ENST00000406610.7	TSL:1 MANE Select	c.3045-22538C>T		intron	N/A	ENSP00000385848.2	Q8TEW8-1
	PARD3B	ENST00000358768.6	TSL:1	c.2859-22538C>T		intron	N/A	ENSP00000351618.2	Q8TEW8-2
	PARD3B	ENST00000351153.5	TSL:1	c.2838-22538C>T		intron	N/A	ENSP00000317261.2	Q8TEW8-6

Frequencies

GnomAD3 genomes AF: 0.139 AC: 21087 AN: 151966 Hom.: 2737 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0950

Gnomad ASJ AF: 0.0806

Gnomad EAS AF: 0.00962

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0598

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.139 AC: 21152 AN: 152084 Hom.: 2753 Cov.: 32 AF XY: 0.134 AC XY: 9946 AN XY: 74354

African (AFR) AF: 0.346 AC: 14352 AN: 41422

American (AMR) AF: 0.0949 AC: 1449 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0806 AC: 280 AN: 3472

East Asian (EAS) AF: 0.00964 AC: 50 AN: 5186

South Asian (SAS) AF: 0.0191 AC: 92 AN: 4826

European-Finnish (FIN) AF: 0.0439 AC: 465 AN: 10588

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0599 AC: 4070 AN: 68000

Other (OTH) AF: 0.123 AC: 260 AN: 2116

Alfa AF: 0.0770 Hom.: 570

Bravo AF: 0.152

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.63
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs13410658; hg19: chr2-206342082;