10-34498163-T-C

Position:

• chr10-34498163-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001184785.2(PARD3):​c.403+18816A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,988 control chromosomes in the GnomAD database, including 23,791 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 0.52 (23791 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.28

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.851 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3	NM_001184785.2	c.403+18816A>G		intron_variant		ENST00000374788.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3	ENST00000374788.8	c.403+18816A>G		intron_variant		1	NM_001184785.2	A1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78247 AN: 151868 Hom.: 23727 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.516 AC: 78375 AN: 151988 Hom.: 23791 Cov.: 32 AF XY: 0.515 AC XY: 38284 AN XY: 74272

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.414

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.360

Gnomad4 OTH AF: 0.466

Alfa AF: 0.491 Hom.: 3834

Bravo AF: 0.531

Asia WGS AF: 0.487 AC: 1686 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.033
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs773991; hg19: chr10-34787091;