Variant chr10-34119708-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001184785.2(PARD3):c.3573A>G(p.Arg1191=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 1,611,624 control chromosomes in the GnomAD database, including 54,002 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.26 ( 5486 hom., cov: 33)

Exomes 𝑓: 0.25 ( 48516 hom. )

Consequence

PARD3
NM_001184785.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.158

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 -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 10-34119708-T-C is Benign according to our data. Variant chr10-34119708-T-C is described in ClinVar as [Benign]. Clinvar id is 3055935.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.158 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3	NM_001184785.2 linkuse as main transcript	c.3573A>G	p.Arg1191=	synonymous_variant	24/25	ENST00000374788.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3	ENST00000374788.8 linkuse as main transcript	c.3573A>G	p.Arg1191=	synonymous_variant	24/25	1	NM_001184785.2	A1	Q8TEW0-2

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39586

AN:

152080

Hom.:

5485

Cov.:

show subpopulations

Gnomad AFR

AF:

0.330

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.232

Gnomad ASJ

AF:

0.295

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.373

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.270

GnomAD3 exomes

AF:

0.218

AC:

53770

AN:

246120

Hom.:

6789

AF XY:

0.220

AC XY:

29387

AN XY:

133792

show subpopulations

Gnomad AFR exome

AF:

0.329

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.304

Gnomad EAS exome

AF:

0.000878

Gnomad SAS exome

AF:

0.164

Gnomad FIN exome

AF:

0.181

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.254

GnomAD4 exome

AF:

0.250

AC:

365367

AN:

1459426

Hom.:

48516

Cov.:

AF XY:

0.248

AC XY:

179981

AN XY:

725900

show subpopulations

Gnomad4 AFR exome

AF:

0.332

Gnomad4 AMR exome

AF:

0.179

Gnomad4 ASJ exome

AF:

0.302

Gnomad4 EAS exome

AF:

0.000680

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.187

Gnomad4 NFE exome

AF:

0.268

Gnomad4 OTH exome

AF:

0.247

GnomAD4 genome

AF:

0.260

AC:

39607

AN:

152198

Hom.:

5486

Cov.:

AF XY:

0.253

AC XY:

18831

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.330

Gnomad4 AMR

AF:

0.232

Gnomad4 ASJ

AF:

0.295

Gnomad4 EAS

AF:

0.00213

Gnomad4 SAS

AF:

0.140

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.264

Hom.:

8759

Bravo

AF:

0.271

Asia WGS

AF:

0.0930

AC:

327

AN:

3478

EpiCase

AF:

0.270

EpiControl

AF:

0.273

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

PARD3-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 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

-0.75

CADD

Benign

7.7

DANN

Benign

0.54

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