rs7075263

Variant names:

• chr10-34739785-T-C
• rs7075263
• NM_001184785.2:c.121-43366A>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.121-43366A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 152,058 control chromosomes in the GnomAD database, including 8,916 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 0.33 (8916 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.121-43366A>G		intron_variant	Intron 1 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.121-43366A>G		intron_variant	Intron 1 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50900 AN: 151940 Hom.: 8913 Cov.: 32

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.335 AC: 50914 AN: 152058 Hom.: 8916 Cov.: 32 AF XY: 0.331 AC XY: 24624 AN XY: 74326

African (AFR) AF: 0.288 AC: 11952 AN: 41474

American (AMR) AF: 0.330 AC: 5037 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1024 AN: 3472

East Asian (EAS) AF: 0.159 AC: 824 AN: 5176

South Asian (SAS) AF: 0.139 AC: 671 AN: 4814

European-Finnish (FIN) AF: 0.394 AC: 4161 AN: 10574

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26090 AN: 67952

Other (OTH) AF: 0.354 AC: 746 AN: 2108

Alfa AF: 0.359 Hom.: 23947

Bravo AF: 0.330

Asia WGS AF: 0.177 AC: 616 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	0.75
DANN	Benign	0.54
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7075263; hg19: chr10-35028713;