NM_178140.4:c.-360-32563T>A

Variant names:

• chr5-31766326-T-A
• rs2059865
• NM_178140.4:c.-360-32563T>A

Variant summary

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

The NM_178140.4(PDZD2):​c.-360-32563T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,154 control chromosomes in the GnomAD database, including 3,765 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 0.19 (3765 hom., cov: 32)
• Consequence: PDZD2 NM_178140.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.220
• Publications: 3 publications found

Genes affected

PDZD2 (HGNC:18486): (PDZ domain containing 2) The protein encoded by this gene contains six PDZ domains and shares sequence similarity with pro-interleukin-16 (pro-IL-16). Like pro-IL-16, the encoded protein localizes to the endoplasmic reticulum and is thought to be cleaved by a caspase to produce a secreted peptide containing two PDZ domains. In addition, this gene is upregulated in primary prostate tumors and may be involved in the early stages of prostate tumorigenesis. [provided by RefSeq, Dec 2015]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PDZD2	NM_178140.4	c.-360-32563T>A		intron_variant	Intron 1 of 24	ENST00000438447.2	NP_835260.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PDZD2	ENST00000438447.2	c.-360-32563T>A		intron_variant	Intron 1 of 24	1	NM_178140.4	ENSP00000402033.1
PDZD2	ENST00000502824.1	n.89-32563T>A		intron_variant	Intron 1 of 2	1
PDZD2	ENST00000513910.1	c.-442-21311T>A		intron_variant	Intron 1 of 2	3		ENSP00000424901.1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29649 AN: 152034 Hom.: 3765 Cov.: 32

Gnomad AFR AF: 0.0506

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.195 AC: 29637 AN: 152154 Hom.: 3765 Cov.: 32 AF XY: 0.194 AC XY: 14432 AN XY: 74380

African (AFR) AF: 0.0504 AC: 2096 AN: 41548

American (AMR) AF: 0.183 AC: 2799 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1203 AN: 3472

East Asian (EAS) AF: 0.00849 AC: 44 AN: 5180

South Asian (SAS) AF: 0.118 AC: 570 AN: 4816

European-Finnish (FIN) AF: 0.288 AC: 3036 AN: 10554

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19140 AN: 67972

Other (OTH) AF: 0.209 AC: 442 AN: 2112

Alfa AF: 0.147 Hom.: 293

Bravo AF: 0.181

Asia WGS AF: 0.0570 AC: 202 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.81
DANN	Benign	0.78
PhyloP100		-0.22
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: rs2059865; hg19: chr5-31766433;