rs779314442
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_014249.4(NR2E3):c.954G>A(p.Thr318=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,828 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. T318T) has been classified as Likely benign.
Frequency
Consequence
NM_014249.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR2E3 | NM_014249.4 | c.954G>A | p.Thr318= | synonymous_variant | 6/8 | ENST00000617575.5 | |
NR2E3 | NM_016346.4 | c.954G>A | p.Thr318= | synonymous_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR2E3 | ENST00000617575.5 | c.954G>A | p.Thr318= | synonymous_variant | 6/8 | 1 | NM_014249.4 | P1 | |
NR2E3 | ENST00000621098.1 | c.954G>A | p.Thr318= | synonymous_variant | 6/7 | 1 | |||
NR2E3 | ENST00000621736.4 | c.690G>A | p.Thr230= | synonymous_variant | 8/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 248420Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134866
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461598Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727092
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at