chr7-128772564-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 Benign (★★). Synonymous variant affecting the same amino acid position (i.e. S338S) has been classified as Likely benign.
Frequency
Consequence
NM_001385125.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OPN1SW | NM_001385125.1 | c.1014G>T | p.Ser338= | synonymous_variant | 5/5 | ENST00000249389.3 | |
CALU | NM_001219.5 | c.*3397C>A | 3_prime_UTR_variant | 7/7 | ENST00000249364.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OPN1SW | ENST00000249389.3 | c.1014G>T | p.Ser338= | synonymous_variant | 5/5 | 1 | NM_001385125.1 | P1 | |
CALU | ENST00000249364.9 | c.*3397C>A | 3_prime_UTR_variant | 7/7 | 1 | NM_001219.5 | |||
CALU | ENST00000449187.7 | c.*3397C>A | 3_prime_UTR_variant | 7/7 | 1 | P1 | |||
CALU | ENST00000542996.7 | c.*3397C>A | 3_prime_UTR_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes AF: 0.00119 AC: 181AN: 152152Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00124 AC: 313AN: 251462Hom.: 1 AF XY: 0.00135 AC XY: 183AN XY: 135908
GnomAD4 exome AF: 0.00121 AC: 1771AN: 1461870Hom.: 5 Cov.: 31 AF XY: 0.00126 AC XY: 918AN XY: 727234
GnomAD4 genome AF: 0.00119 AC: 181AN: 152270Hom.: 2 Cov.: 32 AF XY: 0.00125 AC XY: 93AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:4
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
OPN1SW-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 26, 2020 | This 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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at