rs285589

Variant names:

• chr12-41550605-T-C
• rs285589
• NM_001164595.2:c.1204-2051T>C

Variant summary

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

The NM_001164595.2(PDZRN4):​c.1204-2051T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,068 control chromosomes in the GnomAD database, including 5,120 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 0.23 (5120 hom., cov: 32)
• Consequence: PDZRN4 NM_001164595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.529
• Publications: 2 publications found

Genes affected

PDZRN4 (HGNC:30552): (PDZ domain containing ring finger 4) Predicted to enable metal ion binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000301531 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164595.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDZRN4	NM_001164595.2	MANE Select	c.1204-2051T>C		intron	N/A	NP_001158067.1	Q6ZMN7-1
	PDZRN4	NM_013377.4		c.430-2051T>C		intron	N/A	NP_037509.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDZRN4	ENST00000402685.7	TSL:2 MANE Select	c.1204-2051T>C		intron	N/A	ENSP00000384197.2	Q6ZMN7-1
	PDZRN4	ENST00000539469.6	TSL:1	c.430-2051T>C		intron	N/A	ENSP00000439990.2	Q6ZMN7-2
	PDZRN4	ENST00000548316.1	TSL:1	n.364-2051T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34776 AN: 151948 Hom.: 5118 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.229 AC: 34808 AN: 152068 Hom.: 5120 Cov.: 32 AF XY: 0.226 AC XY: 16819 AN XY: 74350

African (AFR) AF: 0.422 AC: 17502 AN: 41464

American (AMR) AF: 0.228 AC: 3476 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1398 AN: 5152

South Asian (SAS) AF: 0.138 AC: 663 AN: 4820

European-Finnish (FIN) AF: 0.138 AC: 1463 AN: 10592

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9164 AN: 67982

Other (OTH) AF: 0.224 AC: 474 AN: 2112

Alfa AF: 0.197 Hom.: 922

Bravo AF: 0.245

Asia WGS AF: 0.200 AC: 699 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.0
DANN	Benign	0.77
PhyloP100		0.53
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: rs285589; hg19: chr12-41944407;