10-34606401-T-C

Variant names:

• chr10-34606401-T-C
• rs2496720
• NM_001184785.2:c.223-89242A>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.223-89242A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,768 control chromosomes in the GnomAD database, including 1,351 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 0.11 (1351 hom., cov: 27)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.852
• Publications: 7 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 = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.223-89242A>G		intron_variant	Intron 2 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.223-89242A>G		intron_variant	Intron 2 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16686 AN: 151650 Hom.: 1355 Cov.: 27

Gnomad AFR AF: 0.0233

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.179

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.110 AC: 16681 AN: 151768 Hom.: 1351 Cov.: 27 AF XY: 0.114 AC XY: 8449 AN XY: 74142

African (AFR) AF: 0.0232 AC: 963 AN: 41424

American (AMR) AF: 0.152 AC: 2310 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3464

East Asian (EAS) AF: 0.311 AC: 1593 AN: 5124

South Asian (SAS) AF: 0.316 AC: 1507 AN: 4770

European-Finnish (FIN) AF: 0.0914 AC: 963 AN: 10534

Middle Eastern (MID) AF: 0.183 AC: 53 AN: 290

European-Non Finnish (NFE) AF: 0.124 AC: 8391 AN: 67908

Other (OTH) AF: 0.104 AC: 219 AN: 2106

Alfa AF: 0.125 Hom.: 2184

Bravo AF: 0.109

Asia WGS AF: 0.268 AC: 930 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	0.28
DANN	Benign	0.48
PhyloP100		-0.85
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: rs2496720; hg19: chr10-34895329;