rs849230

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001302769.2(PARD3B):​c.2631-4708G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 152,300 control chromosomes in the GnomAD database, including 59,070 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 0.88 ( 59070 hom., cov: 34)

Consequence

PARD3B
NM_001302769.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.67
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PARD3BNM_001302769.2 linkuse as main transcriptc.2631-4708G>A intron_variant ENST00000406610.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PARD3BENST00000406610.7 linkuse as main transcriptc.2631-4708G>A intron_variant 1 NM_001302769.2 P1Q8TEW8-1

Frequencies

GnomAD3 genomes
AF:
0.877
AC:
133517
AN:
152182
Hom.:
59048
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.753
Gnomad AMI
AF:
1.00
Gnomad AMR
AF:
0.928
Gnomad ASJ
AF:
0.925
Gnomad EAS
AF:
0.969
Gnomad SAS
AF:
0.935
Gnomad FIN
AF:
0.956
Gnomad MID
AF:
0.921
Gnomad NFE
AF:
0.914
Gnomad OTH
AF:
0.880
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.877
AC:
133585
AN:
152300
Hom.:
59070
Cov.:
34
AF XY:
0.880
AC XY:
65569
AN XY:
74470
show subpopulations
Gnomad4 AFR
AF:
0.752
Gnomad4 AMR
AF:
0.928
Gnomad4 ASJ
AF:
0.925
Gnomad4 EAS
AF:
0.969
Gnomad4 SAS
AF:
0.934
Gnomad4 FIN
AF:
0.956
Gnomad4 NFE
AF:
0.914
Gnomad4 OTH
AF:
0.881
Alfa
AF:
0.910
Hom.:
26043
Bravo
AF:
0.872
Asia WGS
AF:
0.939
AC:
3265
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.5
DANN
Benign
0.64

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs849230; hg19: chr2-206261029; API