chr10-34493824-C-T

Variant names:

• chr10-34493824-C-T
• rs773985
• NM_001184785.2:c.403+23155G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001184785.2(PARD3):​c.403+23155G>A 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 151,978 control chromosomes in the GnomAD database, including 23,777 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 (23777 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.403+23155G>A		intron_variant	Intron 3 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.403+23155G>A		intron_variant	Intron 3 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78218 AN: 151858 Hom.: 23713 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: 0.416

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.516 AC: 78346 AN: 151978 Hom.: 23777 Cov.: 32 AF XY: 0.515 AC XY: 38273 AN XY: 74266

African (AFR) AF: 0.859 AC: 35621 AN: 41490

American (AMR) AF: 0.434 AC: 6624 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1347 AN: 3466

East Asian (EAS) AF: 0.426 AC: 2199 AN: 5164

South Asian (SAS) AF: 0.415 AC: 1994 AN: 4806

European-Finnish (FIN) AF: 0.446 AC: 4699 AN: 10530

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24407 AN: 67944

Other (OTH) AF: 0.465 AC: 980 AN: 2106

Alfa AF: 0.276 Hom.: 762

Bravo AF: 0.531

Asia WGS AF: 0.486 AC: 1688 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.16
DANN	Benign	0.69
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs773985; hg19: chr10-34782752;