10-34548701-A-T

Position:

• chr10-34548701-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001184785.2(PARD3):​c.223-31542T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,622 control chromosomes in the GnomAD database, including 20,974 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 0.51 (20974 hom., cov: 30)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PARD3	NM_001184785.2	c.223-31542T>A		intron_variant		ENST00000374788.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PARD3	ENST00000374788.8	c.223-31542T>A		intron_variant		1	NM_001184785.2	A1

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76656 AN: 151504 Hom.: 20928 Cov.: 30

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.506 AC: 76759 AN: 151622 Hom.: 20974 Cov.: 30 AF XY: 0.507 AC XY: 37520 AN XY: 74058

Gnomad4 AFR AF: 0.731

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.408

Gnomad4 OTH AF: 0.466

Alfa AF: 0.480 Hom.: 2286

Bravo AF: 0.512

Asia WGS AF: 0.491 AC: 1708 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.78

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

Publications

LitVar

Other links and lift over

dbSNP: rs1657224; hg19: chr10-34837629;