rs6582281

Variant names:

• chr12-41237900-G-A
• rs6582281
• NM_001164595.2:c.843+43712G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-41237900-G-A
• chr12-41237900-G-C
• chr12-41237900-G-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.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
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.712 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.843+43712G>A		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.843+43712G>A		intron	N/A	ENSP00000384197.2	Q6ZMN7-1

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

African (AFR) AF: 0.680 AC: 28194 AN: 41454

American (AMR) AF: 0.724 AC: 11047 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2352 AN: 3464

East Asian (EAS) AF: 0.730 AC: 3764 AN: 5154

South Asian (SAS) AF: 0.733 AC: 3531 AN: 4820

European-Finnish (FIN) AF: 0.662 AC: 6993 AN: 10570

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44039 AN: 67964

Other (OTH) AF: 0.695 AC: 1467 AN: 2112

Alfa AF: 0.583 Hom.: 1966

Bravo AF: 0.680

Asia WGS AF: 0.722 AC: 2509 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.67
PhyloP100		-1.5
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6582281;

hg19: chr12-41631702;