rs10506190

Variant names:

• chr12-41362575-T-C
• rs10506190
• NM_001164595.2:c.844-143881T>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.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
• Publications: 2 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=-0.92).
• 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 rank	MANE	Protein	UniProt
PDZRN4	NM_001164595.2	c.844-143881T>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.844-143881T>C		intron_variant	Intron 3 of 9	2	NM_001164595.2	ENSP00000384197.2

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

African (AFR) AF: 0.0132 AC: 547 AN: 41544

American (AMR) AF: 0.0376 AC: 574 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0548 AC: 190 AN: 3470

East Asian (EAS) AF: 0.000969 AC: 5 AN: 5162

South Asian (SAS) AF: 0.0736 AC: 355 AN: 4824

European-Finnish (FIN) AF: 0.0925 AC: 982 AN: 10614

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0752 AC: 5114 AN: 67962

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0723 Hom.: 557

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
PhyloP100		-2.5
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: rs10506190; hg19: chr12-41756377;