rs10827392

Variant names:

• chr10-34690261-T-C
• rs10827392
• NM_001184785.2:c.222+6057A>G

Variant summary

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

The NM_019619.4(PARD3):​c.222+6057A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,124 control chromosomes in the GnomAD database, including 7,098 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 0.28 (7098 hom., cov: 33)
• Consequence: PARD3 NM_019619.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 3 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019619.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3	NM_001184785.2	MANE Select	c.222+6057A>G		intron	N/A	NP_001171714.1
	PARD3	NM_019619.4		c.222+6057A>G		intron	N/A	NP_062565.2
	PARD3	NM_001184786.2		c.222+6057A>G		intron	N/A	NP_001171715.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3	ENST00000374788.8	TSL:1 MANE Select	c.222+6057A>G		intron	N/A	ENSP00000363920.3
	PARD3	ENST00000374789.8	TSL:1	c.222+6057A>G		intron	N/A	ENSP00000363921.3
	PARD3	ENST00000545693.5	TSL:1	c.222+6057A>G		intron	N/A	ENSP00000443147.1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42129 AN: 152006 Hom.: 7096 Cov.: 33

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.277 AC: 42126 AN: 152124 Hom.: 7098 Cov.: 33 AF XY: 0.275 AC XY: 20469 AN XY: 74346

African (AFR) AF: 0.0973 AC: 4040 AN: 41540

American (AMR) AF: 0.303 AC: 4627 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3472

East Asian (EAS) AF: 0.147 AC: 760 AN: 5166

South Asian (SAS) AF: 0.139 AC: 668 AN: 4816

European-Finnish (FIN) AF: 0.392 AC: 4139 AN: 10568

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25774 AN: 67974

Other (OTH) AF: 0.316 AC: 667 AN: 2110

Alfa AF: 0.308 Hom.: 2751

Bravo AF: 0.265

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.62
PhyloP100		-0.41
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: rs10827392; hg19: chr10-34979189;