1-61914986-C-T

Position:

• chr1-61914986-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.3570+322C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 152,008 control chromosomes in the GnomAD database, including 8,046 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 0.30 (8046 hom., cov: 32)
• Consequence: PATJ NM_001350145.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.960

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PATJ	NM_001350145.3	c.3570+322C>T		intron_variant		ENST00000642238.2	NP_001337074.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PATJ	ENST00000642238.2	c.3570+322C>T		intron_variant			NM_001350145.3	ENSP00000494277.1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45231 AN: 151890 Hom.: 8033 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.298 AC: 45261 AN: 152008 Hom.: 8046 Cov.: 32 AF XY: 0.303 AC XY: 22499 AN XY: 74284

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.313

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.300

Alfa AF: 0.317 Hom.: 11474

Bravo AF: 0.304

Asia WGS AF: 0.527 AC: 1831 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.84

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: rs11207864; hg19: chr1-62380658;