rs10763976

Variant names:

• chr10-34275364-G-A
• rs10763976
• NM_001184785.2:c.3177-5465C>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.3177-5465C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,034 control chromosomes in the GnomAD database, including 13,953 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 0.42 (13953 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.3177-5465C>T		intron_variant	Intron 21 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.3177-5465C>T		intron_variant	Intron 21 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63989 AN: 151916 Hom.: 13948 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.421 AC: 64029 AN: 152034 Hom.: 13953 Cov.: 32 AF XY: 0.424 AC XY: 31464 AN XY: 74290

African (AFR) AF: 0.298 AC: 12356 AN: 41470

American (AMR) AF: 0.432 AC: 6595 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1689 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1785 AN: 5168

South Asian (SAS) AF: 0.517 AC: 2490 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4912 AN: 10544

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32744 AN: 67976

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.471 Hom.: 14102

Bravo AF: 0.411

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.073
DANN	Benign	0.69
PhyloP100		-0.99
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: rs10763976; hg19: chr10-34564292;