rs1805023
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_014249.4(NR2E3):c.694G>A(p.Val232Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00119 in 1,613,730 control chromosomes in the GnomAD database, including 19 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. V232V) has been classified as Uncertain significance.
Frequency
Consequence
NM_014249.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR2E3 | NM_014249.4 | c.694G>A | p.Val232Ile | missense_variant | 5/8 | ENST00000617575.5 | |
NR2E3 | NM_016346.4 | c.694G>A | p.Val232Ile | missense_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR2E3 | ENST00000617575.5 | c.694G>A | p.Val232Ile | missense_variant | 5/8 | 1 | NM_014249.4 | P1 | |
NR2E3 | ENST00000621098.1 | c.694G>A | p.Val232Ile | missense_variant | 5/7 | 1 | |||
NR2E3 | ENST00000621736.4 | c.430G>A | p.Val144Ile | missense_variant | 7/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00628 AC: 956AN: 152110Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00170 AC: 423AN: 248720Hom.: 5 AF XY: 0.00116 AC XY: 156AN XY: 134918
GnomAD4 exome AF: 0.000657 AC: 960AN: 1461502Hom.: 10 Cov.: 33 AF XY: 0.000521 AC XY: 379AN XY: 727032
GnomAD4 genome ? AF: 0.00630 AC: 959AN: 152228Hom.: 9 Cov.: 32 AF XY: 0.00583 AC XY: 434AN XY: 74444
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Enhanced S-cone syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Enhanced S-cone syndrome;C1970163:Retinitis pigmentosa 37 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Counsyl | Jun 13, 2017 | - - |
Retinitis pigmentosa 37 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. - |
Goldmann-Favre syndrome Benign:1
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at