rs10485320

chr6-47809165-T-C

Variant summary

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

The NM_181744.4(OPN5):c.998+770T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,086 control chromosomes in the GnomAD database, including 5,104 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 0.25 (5104 hom., cov: 32)
• Consequence: OPN5 NM_181744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

Genes affected

OPN5 (HGNC:19992): (opsin 5) Opsins are members of the guanine nucleotide-binding protein (G protein)-coupled receptor superfamily. This opsin gene is expressed in the eye, brain, testes, and spinal cord. This gene belongs to the seven-exon subfamily of mammalian opsin genes that includes peropsin (RRH) and retinal G protein coupled receptor (RGR). Like these other seven-exon opsin genes, this family member may encode a protein with photoisomerase activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPN5	NM_181744.4	c.998+770T>C		intron_variant		ENST00000371211.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPN5	ENST00000371211.7	c.998+770T>C		intron_variant		1	NM_181744.4	P4
OPN5	ENST00000244799.4	n.1043+770T>C		intron_variant, non_coding_transcript_variant		1
OPN5	ENST00000393699.2	c.998+770T>C		intron_variant		2		A1
OPN5	ENST00000489301.6	c.998+770T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38759 AN: 151968 Hom.: 5096 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.255 AC: 38780 AN: 152086 Hom.: 5104 Cov.: 32 AF XY: 0.256 AC XY: 19057 AN XY: 74352

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.235

Alfa AF: 0.273 Hom.: 5506

Bravo AF: 0.244

Asia WGS AF: 0.207 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.0
Dann	Benign	0.83

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: rs10485320; hg19: chr6-47776901;