rs3790577

chr1-61791551-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PATJ	NM_001350145.3	c.1168+104A>G		intron_variant		ENST00000642238.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PATJ	ENST00000642238.2	c.1168+104A>G		intron_variant			NM_001350145.3	P1

Frequencies

GnomAD3 genomes AF: 0.441 AC: 67023 AN: 151890 Hom.: 15765 Cov.: 32

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

Gnomad4 AFR exome AF: 0.264

Gnomad4 AMR exome AF: 0.580

Gnomad4 ASJ exome AF: 0.547

Gnomad4 EAS exome AF: 0.391

Gnomad4 SAS exome AF: 0.627

Gnomad4 FIN exome AF: 0.518

Gnomad4 NFE exome AF: 0.486

Gnomad4 OTH exome AF: 0.484

GnomAD4 genome AF: 0.441 AC: 67058 AN: 152008 Hom.: 15777 Cov.: 32 AF XY: 0.448 AC XY: 33295 AN XY: 74272

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.546

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.614

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.457

Alfa AF: 0.490 Hom.: 22857

Bravo AF: 0.431

Asia WGS AF: 0.478 AC: 1660 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
Cadd	Benign	14
Dann	Benign	0.85

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: rs3790577; hg19: chr1-62257223;