Variant chr10-34111165-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2

The NM_001184785.2(PARD3):c.*4C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 1,534,906 control chromosomes in the GnomAD database, including 399 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 25 hom., cov: 32)

Exomes 𝑓: 0.021 ( 374 hom. )

Consequence

PARD3
NM_001184785.2 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0280

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=-0.83).

BP6

Variant 10-34111165-G-A is Benign according to our data. Variant chr10-34111165-G-A is described in ClinVar as [Benign]. Clinvar id is 3056597.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0159 (2418/152284) while in subpopulation NFE AF= 0.0235 (1601/68030). AF 95% confidence interval is 0.0226. There are 25 homozygotes in gnomad4. There are 1191 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 2418 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3	NM_001184785.2 linkuse as main transcript	c.*4C>T		3_prime_UTR_variant	25/25	ENST00000374788.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3	ENST00000374788.8 linkuse as main transcript	c.*4C>T		3_prime_UTR_variant	25/25	1	NM_001184785.2	A1	Q8TEW0-2

Frequencies

GnomAD3 genomes

AF:

0.0159

AC:

2418

AN:

152166

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00401

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0184

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.00807

Gnomad FIN

AF:

0.0243

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0235

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.0168

AC:

3384

AN:

201472

Hom.:

AF XY:

0.0172

AC XY:

1874

AN XY:

109154

show subpopulations

Gnomad AFR exome

AF:

0.00370

Gnomad AMR exome

AF:

0.0102

Gnomad ASJ exome

AF:

0.00892

Gnomad EAS exome

AF:

0.000185

Gnomad SAS exome

AF:

0.00630

Gnomad FIN exome

AF:

0.0255

Gnomad NFE exome

AF:

0.0240

Gnomad OTH exome

AF:

0.0181

GnomAD4 exome

AF:

0.0210

AC:

29065

AN:

1382622

Hom.:

374

Cov.:

AF XY:

0.0208

AC XY:

14120

AN XY:

678958

show subpopulations

Gnomad4 AFR exome

AF:

0.00293

Gnomad4 AMR exome

AF:

0.0100

Gnomad4 ASJ exome

AF:

0.00690

Gnomad4 EAS exome

AF:

0.000104

Gnomad4 SAS exome

AF:

0.00711

Gnomad4 FIN exome

AF:

0.0246

Gnomad4 NFE exome

AF:

0.0240

Gnomad4 OTH exome

AF:

0.0159

GnomAD4 genome

AF:

0.0159

AC:

2418

AN:

152284

Hom.:

Cov.:

AF XY:

0.0160

AC XY:

1191

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00399

Gnomad4 AMR

AF:

0.0184

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00829

Gnomad4 FIN

AF:

0.0243

Gnomad4 NFE

AF:

0.0235

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0143

Hom.:

Bravo

AF:

0.0145

Asia WGS

AF:

0.00520

AC:

AN:

3478

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

Jan 20, 2020

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

-0.83

CADD

Benign

1.5

DANN

Benign

0.76

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