chr10-34328092-C-T

Variant names:

• chr10-34328092-C-T
• rs4379776
• NM_001184785.2:c.2833+3025G>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.2833+3025G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,992 control chromosomes in the GnomAD database, including 12,614 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 0.40 (12614 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 8 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001184785.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3	NM_001184785.2	MANE Select	c.2833+3025G>A		intron	N/A	NP_001171714.1
	PARD3	NM_019619.4		c.2842+3025G>A		intron	N/A	NP_062565.2
	PARD3	NM_001184786.2		c.2794+3025G>A		intron	N/A	NP_001171715.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3	ENST00000374788.8	TSL:1 MANE Select	c.2833+3025G>A		intron	N/A	ENSP00000363920.3
	PARD3	ENST00000374789.8	TSL:1	c.2842+3025G>A		intron	N/A	ENSP00000363921.3
	PARD3	ENST00000545693.5	TSL:1	c.2794+3025G>A		intron	N/A	ENSP00000443147.1

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61364 AN: 151874 Hom.: 12597 Cov.: 32

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.404 AC: 61432 AN: 151992 Hom.: 12614 Cov.: 32 AF XY: 0.407 AC XY: 30198 AN XY: 74280

African (AFR) AF: 0.472 AC: 19569 AN: 41482

American (AMR) AF: 0.411 AC: 6262 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1486 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1927 AN: 5154

South Asian (SAS) AF: 0.486 AC: 2337 AN: 4810

European-Finnish (FIN) AF: 0.377 AC: 3980 AN: 10546

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24668 AN: 67962

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.394 Hom.: 1556

Bravo AF: 0.410

Asia WGS AF: 0.442 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.57
DANN	Benign	0.53
PhyloP100		-0.19
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: rs4379776; hg19: chr10-34617020;