1-62141021-C-T

Variant summary

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

The NM_001350145.3(PATJ):c.5272-7263C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.764 in 151,706 control chromosomes in the GnomAD database, including 44,999 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 0.76 (44999 hom., cov: 28)
• Consequence: PATJ NM_001350145.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12

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 -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 = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PATJ	NM_001350145.3	c.5272-7263C>T		intron_variant		ENST00000642238.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PATJ	ENST00000642238.2	c.5272-7263C>T		intron_variant			NM_001350145.3	P1

Frequencies

GnomAD3 genomes AF: 0.764 AC: 115801 AN: 151588 Hom.: 44939 Cov.: 28

Gnomad AFR AF: 0.895

Gnomad AMI AF: 0.831

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.764 AC: 115924 AN: 151706 Hom.: 44999 Cov.: 28 AF XY: 0.761 AC XY: 56389 AN XY: 74118

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.796

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.760

Alfa AF: 0.716 Hom.: 61625

Bravo AF: 0.787

Asia WGS AF: 0.813 AC: 2823 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	0.57
Dann	Benign	0.63

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: rs2476197; hg19: chr1-62606693;