dbSNP rs3790577: PATJ:c.1168+104A>G (chr1-61791551-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001350145.3(PATJ):c.1168+104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 673,330 control chromosomes in the GnomAD database, including 81,720 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 0.44 ( 15777 hom., cov: 32)

Exomes 𝑓: 0.49 ( 65943 hom. )

Consequence

PATJ
NM_001350145.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.03

Publications

5 publications found

Variant links:

Genes affected

PATJ (HGNC:28881): (PATJ crumbs cell polarity complex component) This gene encodes a protein with multiple PDZ domains. PDZ domains mediate protein-protein interactions, and proteins with multiple PDZ domains often organize multimeric complexes at the plasma membrane. This protein localizes to tight junctions and to the apical membrane of epithelial cells. A similar protein in Drosophila is a scaffolding protein which tethers several members of a multimeric signaling complex in photoreceptors. [provided by RefSeq, Jul 2008]

PATJ links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.26).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.595 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001350145.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PATJ	NM_001350145.3	MANE Select	c.1168+104A>G		intron	N/A	NP_001337074.2	A0A2R8Y549
	PATJ	NM_176877.5		c.1168+104A>G		intron	N/A	NP_795352.3	Q8NI35-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PATJ	ENST00000642238.2	MANE Select	c.1168+104A>G	intron	N/A	ENSP00000494277.1	A0A2R8Y549
PATJ	ENST00000459752.5	TSL:1	n.1282+104A>G	intron	N/A
PATJ	ENST00000484562.5	TSL:1	n.1282+104A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.441

AC:

67023

AN:

151890

Hom.:

15765

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.423

Gnomad AMR

AF:

0.527

Gnomad ASJ

AF:

0.546

Gnomad EAS

AF:

0.422

Gnomad SAS

AF:

0.613

Gnomad FIN

AF:

0.531

Gnomad MID

AF:

0.589

Gnomad NFE

AF:

0.493

Gnomad OTH

AF:

0.452

GnomAD4 exome

AF:

0.495

AC:

257890

AN:

521322

Hom.:

65943

AF XY:

0.504

AC XY:

139518

AN XY:

277074

show subpopulations

African (AFR)

AF:

0.264

AC:

3607

AN:

13670

American (AMR)

AF:

0.580

AC:

12191

AN:

21004

Ashkenazi Jewish (ASJ)

AF:

0.547

AC:

7988

AN:

14590

East Asian (EAS)

AF:

0.391

AC:

11894

AN:

30408

South Asian (SAS)

AF:

0.627

AC:

28226

AN:

45040

European-Finnish (FIN)

AF:

0.518

AC:

19012

AN:

36688

Middle Eastern (MID)

AF:

0.559

AC:

1166

AN:

2086

European-Non Finnish (NFE)

AF:

0.486

AC:

160389

AN:

330108

Other (OTH)

AF:

0.484

AC:

13417

AN:

27728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

5942

11883

17825

23766

29708

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1774

3548

5322

7096

8870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.441

AC:

67058

AN:

152008

Hom.:

15777

Cov.:

AF XY:

0.448

AC XY:

33295

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.273

AC:

11335

AN:

41474

American (AMR)

AF:

0.527

AC:

8040

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.546

AC:

1893

AN:

3468

East Asian (EAS)

AF:

0.421

AC:

2174

AN:

5170

South Asian (SAS)

AF:

0.614

AC:

2960

AN:

4822

European-Finnish (FIN)

AF:

0.531

AC:

5596

AN:

10538

Middle Eastern (MID)

AF:

0.588

AC:

173

AN:

294

European-Non Finnish (NFE)

AF:

0.493

AC:

33535

AN:

67962

Other (OTH)

AF:

0.457

AC:

967

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1853

3706

5558

7411

9264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

626

1252

1878

2504

3130

<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:

0.487

Hom.:

29656

Bravo

AF:

0.431

Asia WGS

AF:

0.478

AC:

1660

AN:

3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.26

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

1.0

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over