rs7568370

Variant names:

• chr2-205034367-T-C
• rs7568370
• NM_001302769.2:c.395-13214T>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.395-13214T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,040 control chromosomes in the GnomAD database, including 23,554 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 0.55 (23554 hom., cov: 33)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.736
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.395-13214T>C		intron_variant	Intron 3 of 22	ENST00000406610.7	NP_001289698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3B	ENST00000406610.7	c.395-13214T>C		intron_variant	Intron 3 of 22	1	NM_001302769.2	ENSP00000385848.2

Frequencies

GnomAD3 genomes AF: 0.551 AC: 83699 AN: 151922 Hom.: 23551 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.551 AC: 83720 AN: 152040 Hom.: 23554 Cov.: 33 AF XY: 0.551 AC XY: 40897 AN XY: 74284

African (AFR) AF: 0.476 AC: 19736 AN: 41458

American (AMR) AF: 0.455 AC: 6939 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2384 AN: 3470

East Asian (EAS) AF: 0.484 AC: 2501 AN: 5164

South Asian (SAS) AF: 0.637 AC: 3072 AN: 4822

European-Finnish (FIN) AF: 0.605 AC: 6400 AN: 10570

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40767 AN: 67982

Other (OTH) AF: 0.590 AC: 1244 AN: 2110

Alfa AF: 0.568 Hom.: 9593

Bravo AF: 0.533

Asia WGS AF: 0.538 AC: 1871 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	11
DANN	Benign	0.68
PhyloP100		0.74
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: rs7568370; hg19: chr2-205899090;