10-34147947-G-A

Variant names:

• chr10-34147947-G-A
• rs650212
• NM_001184785.2:c.3420-16364C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001184785.2(PARD3):​c.3420-16364C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,974 control chromosomes in the GnomAD database, including 5,340 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 (5340 hom., cov: 31)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 0 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 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.3420-16364C>T		intron	N/A	NP_001171714.1
	PARD3	NM_019619.4		c.3429-16364C>T		intron	N/A	NP_062565.2
	PARD3	NM_001184786.2		c.3381-16364C>T		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.3420-16364C>T		intron	N/A	ENSP00000363920.3
	PARD3	ENST00000374789.8	TSL:1	c.3429-16364C>T		intron	N/A	ENSP00000363921.3
	PARD3	ENST00000545693.5	TSL:1	c.3381-16364C>T		intron	N/A	ENSP00000443147.1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35617 AN: 151856 Hom.: 5341 Cov.: 31

Gnomad AFR AF: 0.0702

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.234 AC: 35622 AN: 151974 Hom.: 5340 Cov.: 31 AF XY: 0.235 AC XY: 17452 AN XY: 74264

African (AFR) AF: 0.0700 AC: 2904 AN: 41502

American (AMR) AF: 0.180 AC: 2752 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1103 AN: 3470

East Asian (EAS) AF: 0.137 AC: 706 AN: 5160

South Asian (SAS) AF: 0.181 AC: 873 AN: 4810

European-Finnish (FIN) AF: 0.441 AC: 4638 AN: 10524

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21724 AN: 67918

Other (OTH) AF: 0.232 AC: 490 AN: 2112

Alfa AF: 0.272 Hom.: 821

Bravo AF: 0.210

Asia WGS AF: 0.146 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	19
DANN	Benign	0.79
PhyloP100		2.1
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: rs650212; hg19: chr10-34436875;