rs1929095

chr1-186443589-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002597.5(PDC):c.*390A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 158,250 control chromosomes in the GnomAD database, including 4,663 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 0.20 (4571 hom., cov: 32)
  • Exomes 𝑓: 0.14 (92 hom.)
• Consequence: PDC NM_002597.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310

Genes affected

PDC (HGNC:8759): (phosducin) This gene encodes a phosphoprotein, which is located in the outer and inner segments of the rod cells in the retina. This protein may participate in the regulation of visual phototransduction or in the integration of photoreceptor metabolism. It modulates the phototransduction cascade by interacting with the beta and gamma subunits of the retinal G-protein transducin. This gene is a potential candidate gene for retinitis pigmentosa and Usher syndrome type II. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

PDC-AS1 (HGNC:40432): (PDC antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PDC	NM_002597.5	c.*390A>G		3_prime_UTR_variant	4/4	ENST00000391997.3
PDC-AS1	NR_126002.1	n.345+7016T>C		intron_variant, non_coding_transcript_variant
PDC	NM_022576.4	c.*390A>G		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PDC	ENST00000391997.3	c.*390A>G		3_prime_UTR_variant	4/4	1	NM_002597.5	P1

Frequencies

GnomAD3 genomes AF: 0.204 AC: 30994 AN: 151960 Hom.: 4547 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0680

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.198

GnomAD4 exome AF: 0.141 AC: 870 AN: 6172 Hom.: 92 Cov.: 0 AF XY: 0.142 AC XY: 451 AN XY: 3172

Gnomad4 AFR exome AF: 0.373

Gnomad4 AMR exome AF: 0.171

Gnomad4 ASJ exome AF: 0.263

Gnomad4 EAS exome AF: 0.0451

Gnomad4 SAS exome AF: 0.133

Gnomad4 FIN exome AF: 0.0942

Gnomad4 NFE exome AF: 0.129

Gnomad4 OTH exome AF: 0.156

GnomAD4 genome AF: 0.204 AC: 31059 AN: 152078 Hom.: 4571 Cov.: 32 AF XY: 0.198 AC XY: 14735 AN XY: 74356

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.0402

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0680

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.201

Alfa AF: 0.169 Hom.: 916

Bravo AF: 0.222

Asia WGS AF: 0.134 AC: 464 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	9.2
Dann	Benign	0.86

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

Publications

LitVar

Other links and lift over

dbSNP: rs1929095; hg19: chr1-186412721;