NM_001164595.2:c.843+133245A>C

Variant names:

• chr12-41327433-A-C
• rs1880889
• NM_001164595.2:c.843+133245A>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.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
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PDZRN4	NM_001164595.2	c.843+133245A>C		intron_variant	Intron 3 of 9	ENST00000402685.7	NP_001158067.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZRN4	ENST00000402685.7	c.843+133245A>C		intron_variant	Intron 3 of 9	2	NM_001164595.2	ENSP00000384197.2

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

African (AFR) AF: 0.774 AC: 32127 AN: 41514

American (AMR) AF: 0.948 AC: 14493 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3316 AN: 3470

East Asian (EAS) AF: 0.820 AC: 4248 AN: 5178

South Asian (SAS) AF: 0.888 AC: 4283 AN: 4824

European-Finnish (FIN) AF: 0.966 AC: 10259 AN: 10624

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66496 AN: 68048

Other (OTH) AF: 0.924 AC: 1956 AN: 2116

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
PhyloP100		-0.077
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: rs1880889; hg19: chr12-41721235;