rs4675490

Variant names:

• chr2-205077837-A-G
• rs4675490
• NM_001302769.2:c.505-26589A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-205077837-A-G
• chr2-205077837-A-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.505-26589A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 151,944 control chromosomes in the GnomAD database, including 13,105 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 0.41 (13105 hom., cov: 31)
• Consequence: PARD3B NM_001302769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.931
• Publications: 6 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3B	NM_001302769.2	c.505-26589A>G		intron_variant	Intron 4 of 22	ENST00000406610.7	NP_001289698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3B	ENST00000406610.7	c.505-26589A>G		intron_variant	Intron 4 of 22	1	NM_001302769.2	ENSP00000385848.2
PARD3B	ENST00000358768.6	c.505-26589A>G		intron_variant	Intron 4 of 21	1		ENSP00000351618.2
PARD3B	ENST00000351153.5	c.505-26589A>G		intron_variant	Intron 4 of 21	1		ENSP00000317261.2
PARD3B	ENST00000349953.7	c.505-26589A>G		intron_variant	Intron 4 of 21	1		ENSP00000340280.3

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62160 AN: 151828 Hom.: 13091 Cov.: 31

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.409 AC: 62215 AN: 151944 Hom.: 13105 Cov.: 31 AF XY: 0.413 AC XY: 30641 AN XY: 74262

African (AFR) AF: 0.341 AC: 14124 AN: 41464

American (AMR) AF: 0.535 AC: 8176 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1097 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2873 AN: 5152

South Asian (SAS) AF: 0.421 AC: 2026 AN: 4808

European-Finnish (FIN) AF: 0.410 AC: 4315 AN: 10524

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28276 AN: 67936

Other (OTH) AF: 0.385 AC: 812 AN: 2108

Alfa AF: 0.413 Hom.: 56936

Bravo AF: 0.416

Asia WGS AF: 0.500 AC: 1735 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.71
PhyloP100		0.93
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: rs4675490; hg19: chr2-205942560;