1-186444582-G-T

Variant names:

• chr1-186444582-G-T
• rs11812050
• NM_002597.5:c.214-76C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_002597.5(PDC):​c.214-76C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PDC NM_002597.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 6 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDC	NM_002597.5	MANE Select	c.214-76C>A		intron	N/A	NP_002588.3
	PDC	NM_022576.4		c.58-76C>A		intron	N/A	NP_072098.1
	PDC-AS1	NR_126002.1		n.346-6597G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PDC	ENST00000391997.3	TSL:1 MANE Select	c.214-76C>A		intron	N/A	ENSP00000375855.2
	PDC	ENST00000497198.1	TSL:1	c.58-76C>A		intron	N/A	ENSP00000422775.1
	PDC-AS1	ENST00000622121.1	TSL:4	n.346-6597G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 790304 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 404364

African (AFR) AF: 0.00 AC: 0 AN: 18956

American (AMR) AF: 0.00 AC: 0 AN: 23686

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16790

East Asian (EAS) AF: 0.00 AC: 0 AN: 33572

South Asian (SAS) AF: 0.00 AC: 0 AN: 54870

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34030

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4110

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 566832

Other (OTH) AF: 0.00 AC: 0 AN: 37458

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 44

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		0.055

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: rs11812050; hg19: chr1-186413714;