chr10-34294769-G-A

Variant names:

• chr10-34294769-G-A
• rs1441027
• NM_001184785.2:c.3066-10524C>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.3066-10524C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 151,970 control chromosomes in the GnomAD database, including 18,269 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 0.49 (18269 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.833
• Publications: 4 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.3066-10524C>T		intron_variant	Intron 20 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.3066-10524C>T		intron_variant	Intron 20 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74270 AN: 151850 Hom.: 18253 Cov.: 32

Gnomad AFR AF: 0.484

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.473

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.554

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.489 AC: 74326 AN: 151970 Hom.: 18269 Cov.: 32 AF XY: 0.489 AC XY: 36332 AN XY: 74264

African (AFR) AF: 0.484 AC: 20046 AN: 41434

American (AMR) AF: 0.473 AC: 7218 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1863 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1967 AN: 5152

South Asian (SAS) AF: 0.552 AC: 2657 AN: 4810

European-Finnish (FIN) AF: 0.490 AC: 5174 AN: 10564

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33743 AN: 67960

Other (OTH) AF: 0.512 AC: 1081 AN: 2112

Alfa AF: 0.499 Hom.: 24239

Bravo AF: 0.488

Asia WGS AF: 0.485 AC: 1684 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.0
DANN	Benign	0.63
PhyloP100		0.83
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: rs1441027; hg19: chr10-34583697;