12-41353626-C-T

Variant names:

• chr12-41353626-C-T
• rs10785246
• NM_001164595.2:c.844-152830C>T

Variant summary

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

The NM_001164595.2(PDZRN4):​c.844-152830C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.892 in 151,960 control chromosomes in the GnomAD database, including 60,748 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 0.89 (60748 hom., cov: 30)
• Consequence: PDZRN4 NM_001164595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.924 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.844-152830C>T		intron	N/A	NP_001158067.1	Q6ZMN7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDZRN4	ENST00000402685.7	TSL:2 MANE Select	c.844-152830C>T		intron	N/A	ENSP00000384197.2	Q6ZMN7-1

Frequencies

GnomAD3 genomes AF: 0.892 AC: 135493 AN: 151842 Hom.: 60701 Cov.: 30

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.930

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.892 AC: 135595 AN: 151960 Hom.: 60748 Cov.: 30 AF XY: 0.893 AC XY: 66332 AN XY: 74260

African (AFR) AF: 0.812 AC: 33644 AN: 41416

American (AMR) AF: 0.930 AC: 14160 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3013 AN: 3470

East Asian (EAS) AF: 0.850 AC: 4359 AN: 5126

South Asian (SAS) AF: 0.842 AC: 4065 AN: 4826

European-Finnish (FIN) AF: 0.952 AC: 10100 AN: 10610

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.930 AC: 63184 AN: 67962

Other (OTH) AF: 0.900 AC: 1903 AN: 2114

Alfa AF: 0.913 Hom.: 210973

Bravo AF: 0.889

Asia WGS AF: 0.850 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.033
DANN	Benign	0.26
PhyloP100		-0.93
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: rs10785246; hg19: chr12-41747428;