rs1274466

Positions:

• chr10-34181276-C-T

Variant summary

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

The NM_001184785.2(PARD3):​c.3420-49693G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,010 control chromosomes in the GnomAD database, including 24,462 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 0.56 (24462 hom., cov: 33)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.699

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.3420-49693G>A		intron_variant		ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.3420-49693G>A		intron_variant		1	NM_001184785.2	ENSP00000363920	A1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85376 AN: 151888 Hom.: 24439 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.562 AC: 85450 AN: 152010 Hom.: 24462 Cov.: 33 AF XY: 0.554 AC XY: 41144 AN XY: 74284

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.328

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.547

Alfa AF: 0.551 Hom.: 30442

Bravo AF: 0.564

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.26

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: rs1274466; hg19: chr10-34470204;