chr1-62052275-C-T

Variant names:

• chr1-62052275-C-T
• rs991007
• NM_001350145.3:c.4125+1217C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001350145.3(PATJ):​c.4125+1217C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,032 control chromosomes in the GnomAD database, including 722 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 0.091 (722 hom., cov: 31)
• Consequence: PATJ NM_001350145.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PATJ	NM_001350145.3	c.4125+1217C>T		intron_variant	Intron 31 of 43	ENST00000642238.2	NP_001337074.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PATJ	ENST00000642238.2	c.4125+1217C>T		intron_variant	Intron 31 of 43		NM_001350145.3	ENSP00000494277.1

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13826 AN: 151914 Hom.: 720 Cov.: 31

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.0695

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.0125

Gnomad SAS AF: 0.0931

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.114

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.0910 AC: 13835 AN: 152032 Hom.: 722 Cov.: 31 AF XY: 0.0905 AC XY: 6721 AN XY: 74304

African (AFR) AF: 0.0619 AC: 2566 AN: 41480

American (AMR) AF: 0.0696 AC: 1063 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.0123 AC: 64 AN: 5188

South Asian (SAS) AF: 0.0927 AC: 446 AN: 4810

European-Finnish (FIN) AF: 0.134 AC: 1415 AN: 10522

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.114 AC: 7778 AN: 67978

Other (OTH) AF: 0.0825 AC: 174 AN: 2108

Alfa AF: 0.0873 Hom.: 623

Bravo AF: 0.0831

Asia WGS AF: 0.0730 AC: 253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.7
DANN	Benign	0.59
PhyloP100		0.65
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs991007; hg19: chr1-62517947; COSMIC: COSV56248380;