rs2245124

Variant names:

• chr10-34699527-G-C
• rs2245124
• NM_001184785.2:c.121-3108C>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.121-3108C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,010 control chromosomes in the GnomAD database, including 27,740 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 0.59 (27740 hom., cov: 31)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.121-3108C>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.121-3108C>G		intron_variant	Intron 1 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89481 AN: 151892 Hom.: 27724 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.589 AC: 89545 AN: 152010 Hom.: 27740 Cov.: 31 AF XY: 0.592 AC XY: 43976 AN XY: 74276

African (AFR) AF: 0.402 AC: 16634 AN: 41420

American (AMR) AF: 0.643 AC: 9820 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2165 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2509 AN: 5158

South Asian (SAS) AF: 0.514 AC: 2474 AN: 4814

European-Finnish (FIN) AF: 0.777 AC: 8217 AN: 10570

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45706 AN: 67988

Other (OTH) AF: 0.600 AC: 1268 AN: 2112

Alfa AF: 0.626 Hom.: 3856

Bravo AF: 0.572

Asia WGS AF: 0.562 AC: 1950 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.29
PhyloP100		-0.068
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: rs2245124; hg19: chr10-34988455;