rs10827337

Variant names:

• chr10-34202922-G-A
• rs10827337
• NM_001184785.2:c.3419+66735C>T

Variant summary

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

The ENST00000374788.8(PARD3):​c.3419+66735C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,096 control chromosomes in the GnomAD database, including 3,159 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 (3159 hom., cov: 32)
• Consequence: PARD3 ENST00000374788.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.75
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000374788.8. 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.3419+66735C>T		intron	N/A	NP_001171714.1
	PARD3	NM_019619.4		c.3428+66735C>T		intron	N/A	NP_062565.2
	PARD3	NM_001184786.2		c.3380+66735C>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.3419+66735C>T		intron	N/A	ENSP00000363920.3
	PARD3	ENST00000374789.8	TSL:1	c.3428+66735C>T		intron	N/A	ENSP00000363921.3
	PARD3	ENST00000545693.5	TSL:1	c.3380+66735C>T		intron	N/A	ENSP00000443147.1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30431 AN: 151974 Hom.: 3157 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.200 AC: 30453 AN: 152096 Hom.: 3159 Cov.: 32 AF XY: 0.196 AC XY: 14543 AN XY: 74352

African (AFR) AF: 0.204 AC: 8447 AN: 41492

American (AMR) AF: 0.195 AC: 2972 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 914 AN: 3468

East Asian (EAS) AF: 0.149 AC: 771 AN: 5164

South Asian (SAS) AF: 0.171 AC: 821 AN: 4814

European-Finnish (FIN) AF: 0.128 AC: 1359 AN: 10584

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14535 AN: 67988

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.214 Hom.: 13432

Bravo AF: 0.208

Asia WGS AF: 0.164 AC: 571 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.21
PhyloP100		1.8
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: rs10827337; hg19: chr10-34491850;