chr1-241616905-A-G

Variant names:

• chr1-241616905-A-G
• rs6660991
• NM_014322.3:c.374-12326T>C

Variant summary

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

The NM_014322.3(OPN3):​c.374-12326T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,248 control chromosomes in the GnomAD database, including 789 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 0.091 (789 hom., cov: 32)
• Consequence: OPN3 NM_014322.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 1 publications found

Genes affected

OPN3 (HGNC:14007): (opsin 3) Opsins are members of the guanine nucleotide-binding protein (G protein)-coupled receptor superfamily. In addition to the visual opsins, mammals possess several photoreceptive non-visual opsins that are expressed in extraocular tissues. This gene, opsin 3, is strongly expressed in brain and testis and weakly expressed in liver, placenta, heart, lung, skeletal muscle, kidney, and pancreas. The gene may also be expressed in the retina. The protein has the canonical features of a photoreceptive opsin protein. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
OPN3	NM_014322.3	c.374-12326T>C		intron_variant	Intron 1 of 3	ENST00000366554.3	NP_055137.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
OPN3	ENST00000366554.3	c.374-12326T>C		intron_variant	Intron 1 of 3	1	NM_014322.3	ENSP00000355512.2

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13846 AN: 152130 Hom.: 787 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0330

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.0525

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0622

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0910 AC: 13857 AN: 152248 Hom.: 789 Cov.: 32 AF XY: 0.0904 AC XY: 6731 AN XY: 74442

African (AFR) AF: 0.159 AC: 6622 AN: 41518

American (AMR) AF: 0.0608 AC: 930 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3470

East Asian (EAS) AF: 0.0524 AC: 272 AN: 5186

South Asian (SAS) AF: 0.0804 AC: 388 AN: 4824

European-Finnish (FIN) AF: 0.0894 AC: 949 AN: 10610

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4232 AN: 68022

Other (OTH) AF: 0.0785 AC: 166 AN: 2114

Alfa AF: 0.0686 Hom.: 453

Bravo AF: 0.0913

Asia WGS AF: 0.0700 AC: 248 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.67
PhyloP100		0.016
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: rs6660991; hg19: chr1-241780207;