rs6582281

chr12-41237900-G-Achr12-41237900-G-Cchr12-41237900-G-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+43712G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 152,008 control chromosomes in the GnomAD database, including 34,566 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 0.67 (34566 hom., cov: 32)
• Consequence: PDZRN4 NM_001164595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDZRN4	NM_001164595.2	c.843+43712G>A		intron_variant		ENST00000402685.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDZRN4	ENST00000402685.7	c.843+43712G>A		intron_variant		2	NM_001164595.2	P1

Frequencies

GnomAD3 genomes AF: 0.673 AC: 102218 AN: 151890 Hom.: 34535 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.730

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.692

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

GnomAD4 genome AF: 0.673 AC: 102305 AN: 152008 Hom.: 34566 Cov.: 32 AF XY: 0.674 AC XY: 50106 AN XY: 74298

Gnomad4 AFR AF: 0.680

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.679

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.695

Alfa AF: 0.578 Hom.: 1791

Bravo AF: 0.680

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.42
Dann	Benign	0.67

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: rs6582281; hg19: chr12-41631702;