5-93585083-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_005654.6(NR2F1):c.60C>T(p.Pro20=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000196 in 1,021,420 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. P20P) has been classified as Likely benign.
Frequency
Consequence
NM_005654.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NR2F1 | NM_005654.6 | c.60C>T | p.Pro20= | synonymous_variant | 1/3 | ENST00000327111.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NR2F1 | ENST00000327111.8 | c.60C>T | p.Pro20= | synonymous_variant | 1/3 | 1 | NM_005654.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000687 AC: 1AN: 145584Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.0000217 AC: 19AN: 875836Hom.: 0 Cov.: 30 AF XY: 0.0000170 AC XY: 7AN XY: 412292
GnomAD4 genome ? AF: 0.00000687 AC: 1AN: 145584Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 70816
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at