NM_001184785.2:c.3420-45045G>T

Variant names:

• chr10-34176628-C-A
• rs626394
• NM_001184785.2:c.3420-45045G>T

Variant summary

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

The NM_001184785.2(PARD3):​c.3420-45045G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,144 control chromosomes in the GnomAD database, including 3,783 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 0.20 (3783 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.3420-45045G>T		intron_variant	Intron 22 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.3420-45045G>T		intron_variant	Intron 22 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29916 AN: 152024 Hom.: 3784 Cov.: 32

Gnomad AFR AF: 0.0629

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.197 AC: 29923 AN: 152144 Hom.: 3783 Cov.: 32 AF XY: 0.200 AC XY: 14871 AN XY: 74336

African (AFR) AF: 0.0627 AC: 2605 AN: 41536

American (AMR) AF: 0.151 AC: 2303 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3472

East Asian (EAS) AF: 0.102 AC: 528 AN: 5172

South Asian (SAS) AF: 0.159 AC: 764 AN: 4820

European-Finnish (FIN) AF: 0.414 AC: 4371 AN: 10546

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17818 AN: 67992

Other (OTH) AF: 0.187 AC: 396 AN: 2114

Alfa AF: 0.174 Hom.: 670

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		1.2
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: rs626394; hg19: chr10-34465556;