chr10-34587902-C-T

Variant names:

• chr10-34587902-C-T
• rs1359281
• NM_001184785.2:c.223-70743G>A

Variant summary

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

The NM_001184785.2(PARD3):​c.223-70743G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,990 control chromosomes in the GnomAD database, including 24,464 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 0.53 (24464 hom., cov: 32)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001184785.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3	NM_001184785.2	MANE Select	c.223-70743G>A		intron	N/A	NP_001171714.1
	PARD3	NM_019619.4		c.223-70743G>A		intron	N/A	NP_062565.2
	PARD3	NM_001184786.2		c.223-70743G>A		intron	N/A	NP_001171715.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PARD3	ENST00000374788.8	TSL:1 MANE Select	c.223-70743G>A		intron	N/A	ENSP00000363920.3
	PARD3	ENST00000374789.8	TSL:1	c.223-70743G>A		intron	N/A	ENSP00000363921.3
	PARD3	ENST00000545693.5	TSL:1	c.223-70743G>A		intron	N/A	ENSP00000443147.1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79903 AN: 151870 Hom.: 24399 Cov.: 32

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.527 AC: 80029 AN: 151990 Hom.: 24464 Cov.: 32 AF XY: 0.526 AC XY: 39057 AN XY: 74288

African (AFR) AF: 0.862 AC: 35744 AN: 41476

American (AMR) AF: 0.435 AC: 6644 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1195 AN: 3472

East Asian (EAS) AF: 0.417 AC: 2146 AN: 5150

South Asian (SAS) AF: 0.435 AC: 2088 AN: 4802

European-Finnish (FIN) AF: 0.473 AC: 4993 AN: 10566

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25755 AN: 67940

Other (OTH) AF: 0.472 AC: 995 AN: 2106

Alfa AF: 0.359 Hom.: 1448

Bravo AF: 0.538

Asia WGS AF: 0.484 AC: 1684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.57
PhyloP100		-2.3
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: rs1359281; hg19: chr10-34876830;