chr10-34683859-T-C

Variant names:

• chr10-34683859-T-C
• rs942431
• NM_001184785.2:c.222+12459A>G

Variant summary

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

The NM_001184785.2(PARD3):​c.222+12459A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,068 control chromosomes in the GnomAD database, including 6,866 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 0.30 (6866 hom., cov: 30)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 1 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 (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.222+12459A>G		intron_variant	Intron 2 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.222+12459A>G		intron_variant	Intron 2 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45284 AN: 151950 Hom.: 6858 Cov.: 30

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.298 AC: 45322 AN: 152068 Hom.: 6866 Cov.: 30 AF XY: 0.303 AC XY: 22533 AN XY: 74312

African (AFR) AF: 0.255 AC: 10564 AN: 41488

American (AMR) AF: 0.336 AC: 5130 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3466

East Asian (EAS) AF: 0.343 AC: 1773 AN: 5168

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4814

European-Finnish (FIN) AF: 0.385 AC: 4068 AN: 10560

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19928 AN: 67968

Other (OTH) AF: 0.279 AC: 590 AN: 2112

Alfa AF: 0.308 Hom.: 940

Bravo AF: 0.292

Asia WGS AF: 0.395 AC: 1373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.011
DANN	Benign	0.74
PhyloP100		-2.8
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: rs942431; hg19: chr10-34972787;