rs1880889

chr12-41327433-A-Cchr12-41327433-A-T

Variant summary

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

The NM_001164595.2(PDZRN4):c.843+133245A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 152,260 control chromosomes in the GnomAD database, including 63,508 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 0.91 (63508 hom., cov: 34)
• Consequence: PDZRN4 NM_001164595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDZRN4	NM_001164595.2	c.843+133245A>C		intron_variant		ENST00000402685.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDZRN4	ENST00000402685.7	c.843+133245A>C		intron_variant		2	NM_001164595.2	P1

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138278 AN: 152142 Hom.: 63466 Cov.: 34

Gnomad AFR AF: 0.774

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.909 AC: 138378 AN: 152260 Hom.: 63508 Cov.: 34 AF XY: 0.908 AC XY: 67579 AN XY: 74436

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.948

Gnomad4 ASJ AF: 0.956

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.924

Alfa AF: 0.917 Hom.: 8279

Bravo AF: 0.902

Asia WGS AF: 0.850 AC: 2952 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.8
Dann	Benign	0.77

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: rs1880889; hg19: chr12-41721235;