1-62141021-C-T

Variant names:

• chr1-62141021-C-T
• rs2476197
• NM_001350145.3:c.5272-7263C>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.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
• Publications: 1 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=-0.97).
• 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 rank	MANE	Protein	UniProt
PATJ	NM_001350145.3	c.5272-7263C>T		intron_variant	Intron 41 of 43	ENST00000642238.2	NP_001337074.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PATJ	ENST00000642238.2	c.5272-7263C>T		intron_variant	Intron 41 of 43		NM_001350145.3	ENSP00000494277.1

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

African (AFR) AF: 0.896 AC: 37060 AN: 41384

American (AMR) AF: 0.795 AC: 12110 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2735 AN: 3468

East Asian (EAS) AF: 0.823 AC: 4198 AN: 5100

South Asian (SAS) AF: 0.796 AC: 3818 AN: 4796

European-Finnish (FIN) AF: 0.568 AC: 5972 AN: 10520

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47469 AN: 67890

Other (OTH) AF: 0.760 AC: 1602 AN: 2108

Alfa AF: 0.724 Hom.: 146960

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
PhyloP100		-1.1
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: rs2476197; hg19: chr1-62606693;