rs4557101

Variant names:

• chr3-73491467-T-C
• rs4557101
• NM_015009.3:c.919-87072A>G

Variant summary

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

The NM_015009.3(PDZRN3):​c.919-87072A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 152,008 control chromosomes in the GnomAD database, including 7,112 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 0.29 (7112 hom., cov: 31)
• Consequence: PDZRN3 NM_015009.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.401
• Publications: 10 publications found

Genes affected

PDZRN3 (HGNC:17704): (PDZ domain containing ring finger 3) This gene encodes a member of the LNX (Ligand of Numb Protein-X) family of RING-type ubiquitin E3 ligases. This protein may function in vascular morphogenesis and the differentiation of adipocytes, osteoblasts and myoblasts. This protein may be targeted for degradation by the human papilloma virus E6 protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDZRN3	NM_015009.3	c.919-87072A>G		intron_variant	Intron 3 of 9	ENST00000263666.9	NP_055824.1
PDZRN3	NM_001303139.2	c.12+77684A>G		intron_variant	Intron 1 of 7		NP_001290068.1
PDZRN3	NM_001303140.2	c.-112+69984A>G		intron_variant	Intron 1 of 7		NP_001290069.1
PDZRN3	XM_017005942.3	c.832-87072A>G		intron_variant	Intron 2 of 8		XP_016861431.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZRN3	ENST00000263666.9	c.919-87072A>G		intron_variant	Intron 3 of 9	1	NM_015009.3	ENSP00000263666.4

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44267 AN: 151890 Hom.: 7110 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.291 AC: 44285 AN: 152008 Hom.: 7112 Cov.: 31 AF XY: 0.285 AC XY: 21168 AN XY: 74268

African (AFR) AF: 0.164 AC: 6793 AN: 41440

American (AMR) AF: 0.282 AC: 4307 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3470

East Asian (EAS) AF: 0.128 AC: 663 AN: 5182

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4810

European-Finnish (FIN) AF: 0.302 AC: 3181 AN: 10528

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26079 AN: 67972

Other (OTH) AF: 0.300 AC: 632 AN: 2106

Alfa AF: 0.321 Hom.: 2434

Bravo AF: 0.282

Asia WGS AF: 0.195 AC: 679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.8
DANN	Benign	0.47
PhyloP100		-0.40
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: rs4557101; hg19: chr3-73540618;