chr10-34259167-C-G

Variant names:

• chr10-34259167-C-G
• rs626859
• NM_001184785.2:c.3419+10490G>C

Variant summary

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

The NM_001184785.2(PARD3):​c.3419+10490G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,690 control chromosomes in the GnomAD database, including 26,295 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 0.58 (26295 hom., cov: 31)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.3419+10490G>C		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.3419+10490G>C		intron_variant	Intron 22 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87564 AN: 151570 Hom.: 26250 Cov.: 31

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.654

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.578 AC: 87665 AN: 151690 Hom.: 26295 Cov.: 31 AF XY: 0.574 AC XY: 42552 AN XY: 74092

African (AFR) AF: 0.749 AC: 30976 AN: 41374

American (AMR) AF: 0.511 AC: 7782 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2059 AN: 3464

East Asian (EAS) AF: 0.344 AC: 1771 AN: 5146

South Asian (SAS) AF: 0.545 AC: 2623 AN: 4816

European-Finnish (FIN) AF: 0.469 AC: 4917 AN: 10484

Middle Eastern (MID) AF: 0.672 AC: 195 AN: 290

European-Non Finnish (NFE) AF: 0.527 AC: 35757 AN: 67856

Other (OTH) AF: 0.588 AC: 1239 AN: 2108

Alfa AF: 0.552 Hom.: 2816

Bravo AF: 0.589

Asia WGS AF: 0.498 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.20
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: rs626859; hg19: chr10-34548095;