chr6-47809165-T-C

Variant names:

• chr6-47809165-T-C
• rs10485320
• NM_181744.4:c.998+770T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_181744.4. 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
	OPN5	NM_181744.4	MANE Select	c.998+770T>C		intron	N/A	NP_859528.1	Q6U736
	OPN5	NR_033806.2		n.1043+770T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OPN5	ENST00000371211.7	TSL:1 MANE Select	c.998+770T>C		intron	N/A	ENSP00000360255.2	Q6U736
	OPN5	ENST00000244799.4	TSL:1	n.1043+770T>C		intron	N/A
	OPN5	ENST00000489301.6	TSL:5	c.998+770T>C		intron	N/A	ENSP00000426991.1	D6RDV4

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

African (AFR) AF: 0.223 AC: 9251 AN: 41478

American (AMR) AF: 0.188 AC: 2874 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3468

East Asian (EAS) AF: 0.185 AC: 955 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1388 AN: 4822

European-Finnish (FIN) AF: 0.314 AC: 3322 AN: 10564

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19190 AN: 67986

Other (OTH) AF: 0.235 AC: 496 AN: 2112

Alfa AF: 0.269 Hom.: 7054

Bravo AF: 0.244

Asia WGS AF: 0.207 AC: 720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.83
PhyloP100		-0.23
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: rs10485320; hg19: chr6-47776901;