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GeneBe

7-128772564-C-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS2

The NM_001385125.1(OPN1SW):c.1014G>T(p.Ser338=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,614,140 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S338S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0012 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 5 hom. )

Consequence

OPN1SW
NM_001385125.1 synonymous

Scores

2

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.630
Variant links:
Genes affected
OPN1SW (HGNC:1012): (opsin 1, short wave sensitive) This gene belongs to the G-protein coupled receptor 1 family, opsin subfamily. It encodes the blue cone pigment gene which is one of three types of cone photoreceptors responsible for normal color vision. Defects in this gene are the cause of tritan color blindness (tritanopia). Affected individuals lack blue and yellow sensory mechanisms while retaining those for red and green. Defective blue vision is characteristic. [provided by RefSeq, Jul 2008]
CALU (HGNC:1458): (calumenin) The product of this gene is a calcium-binding protein localized in the endoplasmic reticulum (ER) and it is involved in such ER functions as protein folding and sorting. This protein belongs to a family of multiple EF-hand proteins (CERC) that include reticulocalbin, ERC-55, and Cab45 and the product of this gene. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
Variant 7-128772564-C-A is Benign according to our data. Variant chr7-128772564-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 1167587.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-128772564-C-A is described in Lovd as [Likely_benign].
BP7
Synonymous conserved (PhyloP=0.63 with no splicing effect.
BS2
High AC in GnomAd4 at 181 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
OPN1SWNM_001385125.1 linkuse as main transcriptc.1014G>T p.Ser338= synonymous_variant 5/5 ENST00000249389.3
CALUNM_001219.5 linkuse as main transcriptc.*3397C>A 3_prime_UTR_variant 7/7 ENST00000249364.9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
OPN1SWENST00000249389.3 linkuse as main transcriptc.1014G>T p.Ser338= synonymous_variant 5/51 NM_001385125.1 P1
CALUENST00000249364.9 linkuse as main transcriptc.*3397C>A 3_prime_UTR_variant 7/71 NM_001219.5 O43852-1
CALUENST00000449187.7 linkuse as main transcriptc.*3397C>A 3_prime_UTR_variant 7/71 P1O43852-2
CALUENST00000542996.7 linkuse as main transcriptc.*3397C>A 3_prime_UTR_variant 8/81 O43852-4

Frequencies

GnomAD3 genomes
AF:
0.00119
AC:
181
AN:
152152
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000193
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00308
Gnomad ASJ
AF:
0.00288
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000472
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.00154
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00124
AC:
313
AN:
251462
Hom.:
1
AF XY:
0.00135
AC XY:
183
AN XY:
135908
show subpopulations
Gnomad AFR exome
AF:
0.000185
Gnomad AMR exome
AF:
0.00119
Gnomad ASJ exome
AF:
0.00278
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000915
Gnomad FIN exome
AF:
0.000601
Gnomad NFE exome
AF:
0.00171
Gnomad OTH exome
AF:
0.000977
GnomAD4 exome
AF:
0.00121
AC:
1771
AN:
1461870
Hom.:
5
Cov.:
31
AF XY:
0.00126
AC XY:
918
AN XY:
727234
show subpopulations
Gnomad4 AFR exome
AF:
0.000388
Gnomad4 AMR exome
AF:
0.00121
Gnomad4 ASJ exome
AF:
0.00268
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000672
Gnomad4 FIN exome
AF:
0.000711
Gnomad4 NFE exome
AF:
0.00124
Gnomad4 OTH exome
AF:
0.00180
GnomAD4 genome
AF:
0.00119
AC:
181
AN:
152270
Hom.:
2
Cov.:
32
AF XY:
0.00125
AC XY:
93
AN XY:
74448
show subpopulations
Gnomad4 AFR
AF:
0.000193
Gnomad4 AMR
AF:
0.00307
Gnomad4 ASJ
AF:
0.00288
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000472
Gnomad4 NFE
AF:
0.00154
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.00130
Hom.:
1
Bravo
AF:
0.00106
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.00240
EpiControl
AF:
0.00261

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Likely benign, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Benign, criteria provided, single submitterclinical testingInvitaeJan 29, 2024- -
Likely benign, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
OPN1SW-related disorder Benign:1
Likely benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesFeb 26, 2020This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.37
CADD
Benign
2.1
DANN
Benign
0.77

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs140568559; hg19: chr7-128412618; API