NM_002597.5:c.61+834A>G

Variant names:

• chr1-186448565-T-C
• rs6672836
• NM_002597.5:c.61+834A>G

Variant summary

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

The NM_002597.5(PDC):​c.61+834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 283,448 control chromosomes in the GnomAD database, including 13,989 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 0.33 (9301 hom., cov: 32)
  • Exomes 𝑓: 0.26 (4688 hom.)
• Consequence: PDC NM_002597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50
• Publications: 4 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002597.5. 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
	PDC	NM_002597.5	MANE Select	c.61+834A>G		intron	N/A	NP_002588.3
	PDC	NM_022576.4		c.-96+63A>G		intron	N/A	NP_072098.1	P20941-2
	PDC-AS1	NR_126002.1		n.346-2614T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDC	ENST00000391997.3	TSL:1 MANE Select	c.61+834A>G		intron	N/A	ENSP00000375855.2	P20941-1
	PDC	ENST00000497198.1	TSL:1	c.-96+63A>G		intron	N/A	ENSP00000422775.1	P20941-2
	PDC-AS1	ENST00000622121.1	TSL:4	n.346-2614T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50533 AN: 151826 Hom.: 9258 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.263 AC: 34542 AN: 131502 Hom.: 4688 AF XY: 0.262 AC XY: 16671 AN XY: 63700

African (AFR) AF: 0.507 AC: 1209 AN: 2384

American (AMR) AF: 0.384 AC: 56 AN: 146

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 259 AN: 840

East Asian (EAS) AF: 0.442 AC: 242 AN: 548

South Asian (SAS) AF: 0.262 AC: 668 AN: 2552

European-Finnish (FIN) AF: 0.263 AC: 10 AN: 38

Middle Eastern (MID) AF: 0.292 AC: 70 AN: 240

European-Non Finnish (NFE) AF: 0.256 AC: 30807 AN: 120436

Other (OTH) AF: 0.283 AC: 1221 AN: 4318

GnomAD4 genome AF: 0.333 AC: 50622 AN: 151946 Hom.: 9301 Cov.: 32 AF XY: 0.333 AC XY: 24722 AN XY: 74298

African (AFR) AF: 0.480 AC: 19867 AN: 41412

American (AMR) AF: 0.373 AC: 5698 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1094 AN: 3464

East Asian (EAS) AF: 0.425 AC: 2197 AN: 5166

South Asian (SAS) AF: 0.256 AC: 1236 AN: 4822

European-Finnish (FIN) AF: 0.217 AC: 2298 AN: 10570

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17195 AN: 67934

Other (OTH) AF: 0.348 AC: 735 AN: 2110

Alfa AF: 0.185 Hom.: 482

Bravo AF: 0.358

Asia WGS AF: 0.396 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.42
PhyloP100		-1.5
PromoterAI		0.0068	Neutral
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: rs6672836; hg19: chr1-186417697;