rs1458175

Variant names:

• chr12-41572059-A-C
• rs1458175
• NM_001164595.2:c.1585-305A>C

Your query was ambiguous. Multiple possible variants found:

• chr12-41572059-A-C
• chr12-41572059-A-G
• chr12-41572059-A-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.1585-305A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 151,970 control chromosomes in the GnomAD database, including 27,390 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 0.59 (27390 hom., cov: 32)
• Consequence: PDZRN4 NM_001164595.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.896
• Publications: 18 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]

ENSG00000301531 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDZRN4	NM_001164595.2	c.1585-305A>C		intron_variant	Intron 9 of 9	ENST00000402685.7	NP_001158067.1
PDZRN4	NM_013377.4	c.811-305A>C		intron_variant	Intron 7 of 7		NP_037509.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZRN4	ENST00000402685.7	c.1585-305A>C		intron_variant	Intron 9 of 9	2	NM_001164595.2	ENSP00000384197.2

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90002 AN: 151852 Hom.: 27352 Cov.: 32

Gnomad AFR AF: 0.655

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.593 AC: 90097 AN: 151970 Hom.: 27390 Cov.: 32 AF XY: 0.601 AC XY: 44642 AN XY: 74270

African (AFR) AF: 0.655 AC: 27138 AN: 41424

American (AMR) AF: 0.679 AC: 10386 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1974 AN: 3468

East Asian (EAS) AF: 0.839 AC: 4328 AN: 5160

South Asian (SAS) AF: 0.662 AC: 3191 AN: 4820

European-Finnish (FIN) AF: 0.621 AC: 6545 AN: 10546

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34529 AN: 67944

Other (OTH) AF: 0.601 AC: 1271 AN: 2114

Alfa AF: 0.544 Hom.: 64424

Bravo AF: 0.598

Asia WGS AF: 0.756 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.69
PhyloP100		-0.90
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: rs1458175; hg19: chr12-41965861; COSMIC: COSV54204724;