rs10506190

chr12-41362575-T-C

Variant summary

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

The NM_001164595.2(PDZRN4):c.844-143881T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 152,160 control chromosomes in the GnomAD database, including 319 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 0.053 (319 hom., cov: 32)
• Consequence: PDZRN4 NM_001164595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDZRN4	NM_001164595.2	c.844-143881T>C		intron_variant		ENST00000402685.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDZRN4	ENST00000402685.7	c.844-143881T>C		intron_variant		2	NM_001164595.2	P1

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 8062 AN: 152042 Hom.: 319 Cov.: 32

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.000966

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.0925

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0752

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0529 AC: 8055 AN: 152160 Hom.: 319 Cov.: 32 AF XY: 0.0539 AC XY: 4008 AN XY: 74378

Gnomad4 AFR AF: 0.0132

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.000969

Gnomad4 SAS AF: 0.0736

Gnomad4 FIN AF: 0.0925

Gnomad4 NFE AF: 0.0752

Gnomad4 OTH AF: 0.0553

Alfa AF: 0.0732 Hom.: 495

Bravo AF: 0.0472

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.0030
Dann	Benign	0.51

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: rs10506190; hg19: chr12-41756377;