dbSNP rs647758: PARD3:c.3419+67731T>C (chr10-34201926-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.41

Publications

2 publications found

Variant links:

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]

PARD3 links:

Y_RNA (HGNC:):

Y_RNA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

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

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PARD3	NM_001184785.2	MANE Select	c.3419+67731T>C	intron	N/A	NP_001171714.1	Q8TEW0-2
PARD3	NM_019619.4		c.3428+67731T>C	intron	N/A	NP_062565.2
PARD3	NM_001184786.2		c.3380+67731T>C	intron	N/A	NP_001171715.1	Q8TEW0-11

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PARD3	ENST00000374788.8	TSL:1 MANE Select	c.3419+67731T>C	intron	N/A	ENSP00000363920.3	Q8TEW0-2
PARD3	ENST00000374789.8	TSL:1	c.3428+67731T>C	intron	N/A	ENSP00000363921.3	Q8TEW0-1
PARD3	ENST00000545693.5	TSL:1	c.3380+67731T>C	intron	N/A	ENSP00000443147.1	Q8TEW0-11

Frequencies

GnomAD3 genomes

AF:

0.648

AC:

98519

AN:

151994

Hom.:

32931

Cov.:

show subpopulations

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:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.648

AC:

98606

AN:

152116

Hom.:

32972

Cov.:

AF XY:

0.639

AC XY:

47548

AN XY:

74356

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1685

3369

5054

6738

8423

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

772

1544

2316

3088

3860

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

0.31

(source)

DANN

Benign

0.79

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over