Variant 10-34331292-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_001184785.2(PARD3):c.2658G>A(p.Ser886=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 1,612,910 control chromosomes in the GnomAD database, including 191,218 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.54 ( 22893 hom., cov: 31)

Exomes 𝑓: 0.48 ( 168325 hom. )

Consequence

PARD3
NM_001184785.2 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -3.84

Variant links:

Genes affected

PARD3 (HGNC:16051): (par-3 family cell polarity regulator) This gene encodes a member of the PARD protein family. PARD family members interact with other PARD family members and other proteins; they affect asymmetrical cell division and direct polarized cell growth. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2011]

PARD3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant 10-34331292-C-T is Benign according to our data. Variant chr10-34331292-C-T is described in ClinVar as [Benign]. Clinvar id is 3060980.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-3.84 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARD3	NM_001184785.2 linkuse as main transcript	c.2658G>A	p.Ser886=	synonymous_variant	19/25	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8 linkuse as main transcript	c.2658G>A	p.Ser886=	synonymous_variant	19/25	1	NM_001184785.2	ENSP00000363920	A1	Q8TEW0-2

Frequencies

GnomAD3 genomes

AF:

0.537

AC:

81542

AN:

151722

Hom.:

22842

Cov.:

show subpopulations

Gnomad AFR

AF:

0.701

Gnomad AMI

AF:

0.407

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.530

Gnomad EAS

AF:

0.374

Gnomad SAS

AF:

0.540

Gnomad FIN

AF:

0.482

Gnomad MID

AF:

0.471

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.527

GnomAD3 exomes

AF:

0.490

AC:

122927

AN:

251086

Hom.:

30852

AF XY:

0.488

AC XY:

66267

AN XY:

135682

show subpopulations

Gnomad AFR exome

AF:

0.708

Gnomad AMR exome

AF:

0.480

Gnomad ASJ exome

AF:

0.517

Gnomad EAS exome

AF:

0.373

Gnomad SAS exome

AF:

0.526

Gnomad FIN exome

AF:

0.482

Gnomad NFE exome

AF:

0.469

Gnomad OTH exome

AF:

0.493

GnomAD4 exome

AF:

0.478

AC:

697921

AN:

1461068

Hom.:

168325

Cov.:

AF XY:

0.478

AC XY:

347568

AN XY:

726842

show subpopulations

Gnomad4 AFR exome

AF:

0.710

Gnomad4 AMR exome

AF:

0.483

Gnomad4 ASJ exome

AF:

0.515

Gnomad4 EAS exome

AF:

0.397

Gnomad4 SAS exome

AF:

0.523

Gnomad4 FIN exome

AF:

0.479

Gnomad4 NFE exome

AF:

0.468

Gnomad4 OTH exome

AF:

0.492

GnomAD4 genome

AF:

0.538

AC:

81655

AN:

151842

Hom.:

22893

Cov.:

AF XY:

0.539

AC XY:

40009

AN XY:

74172

show subpopulations

Gnomad4 AFR

AF:

0.701

Gnomad4 AMR

AF:

0.515

Gnomad4 ASJ

AF:

0.530

Gnomad4 EAS

AF:

0.374

Gnomad4 SAS

AF:

0.539

Gnomad4 FIN

AF:

0.482

Gnomad4 NFE

AF:

0.466

Gnomad4 OTH

AF:

0.528

Alfa

AF:

0.485

Hom.:

30969

Bravo

AF:

0.548

Asia WGS

AF:

0.480

AC:

1672

AN:

3478

EpiCase

AF:

0.477

EpiControl

AF:

0.473

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PARD3-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

0.58

DANN

Benign

0.75

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over