chr2-205461868-A-G

Variant names:

• chr2-205461868-A-G
• rs7565154
• NM_001302769.2:c.3044+21196A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302769.2(PARD3B):​c.3044+21196A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,182 control chromosomes in the GnomAD database, including 3,522 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 0.16 (3522 hom., cov: 32)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.3044+21196A>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.3044+21196A>G		intron_variant	Intron 20 of 22	1	NM_001302769.2	ENSP00000385848.2
PARD3B	ENST00000358768.6	c.2858+21196A>G		intron_variant	Intron 19 of 21	1		ENSP00000351618.2
PARD3B	ENST00000351153.5	c.2837+21196A>G		intron_variant	Intron 19 of 21	1		ENSP00000317261.2
PARD3B	ENST00000349953.7	c.2742-38028A>G		intron_variant	Intron 19 of 21	1		ENSP00000340280.3

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24141 AN: 152064 Hom.: 3499 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.0487

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.159 AC: 24211 AN: 152182 Hom.: 3522 Cov.: 32 AF XY: 0.154 AC XY: 11438 AN XY: 74426

African (AFR) AF: 0.392 AC: 16273 AN: 41494

American (AMR) AF: 0.110 AC: 1680 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3468

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5188

South Asian (SAS) AF: 0.0227 AC: 109 AN: 4806

European-Finnish (FIN) AF: 0.0487 AC: 517 AN: 10610

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4808 AN: 68012

Other (OTH) AF: 0.144 AC: 305 AN: 2116

Alfa AF: 0.120 Hom.: 472

Bravo AF: 0.175

Asia WGS AF: 0.0440 AC: 154 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	1.8
DANN	Benign	0.41
PhyloP100		-0.049
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: rs7565154; hg19: chr2-206326592;