chr15-71810734-C-T
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_014249.4(NR2E3):c.-10C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000234 in 1,408,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
NR2E3
NM_014249.4 5_prime_UTR
NM_014249.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.222
Genes affected
NR2E3 (HGNC:7974): (nuclear receptor subfamily 2 group E member 3) This protein is part of a large family of nuclear receptor transcription factors involved in signaling pathways. Nuclear receptors have been shown to regulate pathways involved in embryonic development, as well as in maintenance of proper cell function in adults. Members of this family are characterized by discrete domains that function in DNA and ligand binding. This gene encodes a retinal nuclear receptor that is a ligand-dependent transcription factor. Defects in this gene are a cause of enhanced S cone syndrome. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR2E3 | NM_014249.4 | c.-10C>T | 5_prime_UTR_variant | 1/8 | ENST00000617575.5 | ||
NR2E3 | NM_016346.4 | c.-10C>T | 5_prime_UTR_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR2E3 | ENST00000617575.5 | c.-10C>T | 5_prime_UTR_variant | 1/8 | 1 | NM_014249.4 | P1 | ||
NR2E3 | ENST00000621098.1 | c.-10C>T | 5_prime_UTR_variant | 1/7 | 1 | ||||
NR2E3 | ENST00000621736.4 | c.-146-749C>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.00000595 AC: 1AN: 167930Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 89564
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GnomAD4 exome AF: 0.0000234 AC: 33AN: 1408884Hom.: 0 Cov.: 31 AF XY: 0.0000201 AC XY: 14AN XY: 695926
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GnomAD4 genome Cov.: 32
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Bravo
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Enhanced S-cone syndrome;C1970163:Retinitis pigmentosa 37 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 24, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at