15-71813545-G-A
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2
The NM_014249.4(NR2E3):c.904G>A(p.Val302Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,613,860 control chromosomes in the GnomAD database, including 27 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NR2E3 | NM_014249.4 | c.904G>A | p.Val302Ile | missense_variant | 6/8 | ENST00000617575.5 | NP_055064.1 | |
NR2E3 | NM_016346.4 | c.904G>A | p.Val302Ile | missense_variant | 6/7 | NP_057430.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NR2E3 | ENST00000617575.5 | c.904G>A | p.Val302Ile | missense_variant | 6/8 | 1 | NM_014249.4 | ENSP00000482504.1 | ||
NR2E3 | ENST00000621098.1 | c.904G>A | p.Val302Ile | missense_variant | 6/7 | 1 | ENSP00000479962.1 | |||
NR2E3 | ENST00000621736.4 | c.640G>A | p.Val214Ile | missense_variant | 8/10 | 2 | ENSP00000479254.1 |
Frequencies
GnomAD3 genomes AF: 0.00150 AC: 229AN: 152242Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00379 AC: 941AN: 248526Hom.: 12 AF XY: 0.00426 AC XY: 575AN XY: 134890
GnomAD4 exome AF: 0.00141 AC: 2056AN: 1461500Hom.: 24 Cov.: 32 AF XY: 0.00178 AC XY: 1295AN XY: 727028
GnomAD4 genome AF: 0.00151 AC: 230AN: 152360Hom.: 3 Cov.: 32 AF XY: 0.00188 AC XY: 140AN XY: 74500
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 01, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 04, 2016 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Enhanced S-cone syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 20, 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. - |
Retinitis pigmentosa 37 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 20, 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. - |
Retinal dystrophy Benign:1
Benign, criteria provided, single submitter | research | Dept Of Ophthalmology, Nagoya University | Oct 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at