rs657477

chr10-34220933-T-A

Variant summary

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

The NM_001184785.2(PARD3):c.3419+48724A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,140 control chromosomes in the GnomAD database, including 5,164 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 0.23 (5164 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.76

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3	NM_001184785.2	c.3419+48724A>T		intron_variant		ENST00000374788.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3	ENST00000374788.8	c.3419+48724A>T		intron_variant		1	NM_001184785.2	A1

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35432 AN: 152022 Hom.: 5165 Cov.: 32

Gnomad AFR AF: 0.0793

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0829

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.233 AC: 35426 AN: 152140 Hom.: 5164 Cov.: 32 AF XY: 0.234 AC XY: 17372 AN XY: 74376

Gnomad4 AFR AF: 0.0791

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.0828

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.239

Alfa AF: 0.272 Hom.: 752

Bravo AF: 0.213

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.30
Dann	Benign	0.72

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: rs657477; hg19: chr10-34509861;