rs647758

Variant names:

• chr10-34201926-A-G
• rs647758
• NM_001184785.2:c.3419+67731T>C

Variant summary

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

The NM_001184785.2(PARD3):​c.3419+67731T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,120 control chromosomes in the GnomAD database, including 32,972 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 0.65 (32972 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PARD3 NM_001184785.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 2 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]

Y_RNA (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PARD3	NM_001184785.2	c.3419+67731T>C		intron_variant	Intron 22 of 24	ENST00000374788.8	NP_001171714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PARD3	ENST00000374788.8	c.3419+67731T>C		intron_variant	Intron 22 of 24	1	NM_001184785.2	ENSP00000363920.3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98519 AN: 151994 Hom.: 32931 Cov.: 32

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.637

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.648 AC: 98606 AN: 152116 Hom.: 32972 Cov.: 32 AF XY: 0.639 AC XY: 47548 AN XY: 74356

African (AFR) AF: 0.748 AC: 31049 AN: 41498

American (AMR) AF: 0.565 AC: 8638 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2208 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1233 AN: 5174

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4818

European-Finnish (FIN) AF: 0.676 AC: 7156 AN: 10578

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

European-Non Finnish (NFE) AF: 0.652 AC: 44348 AN: 67972

Other (OTH) AF: 0.631 AC: 1331 AN: 2110

Alfa AF: 0.651 Hom.: 40437

Bravo AF: 0.647

Asia WGS AF: 0.341 AC: 1191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.31
DANN	Benign	0.79
PhyloP100		-1.4
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: rs647758; hg19: chr10-34490854;