rs2245124

Positions:

• chr10-34699527-G-C

Variant summary

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

The NM_001184785.2(PARD3):​c.121-3108C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,010 control chromosomes in the GnomAD database, including 27,740 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 0.59 (27740 hom., cov: 31)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

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 (NFE) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3	NM_001184785.2	c.121-3108C>G		intron_variant		ENST00000374788.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3	ENST00000374788.8	c.121-3108C>G		intron_variant		1	NM_001184785.2	A1

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89481 AN: 151892 Hom.: 27724 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.589 AC: 89545 AN: 152010 Hom.: 27740 Cov.: 31 AF XY: 0.592 AC XY: 43976 AN XY: 74276

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.624

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.777

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.600

Alfa AF: 0.626 Hom.: 3856

Bravo AF: 0.572

Asia WGS AF: 0.562 AC: 1950 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	1.6
DANN	Benign	0.29

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: rs2245124; hg19: chr10-34988455;