2-24665881-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_003743.5(NCOA1):c.222C>T(p.Val74Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,591,076 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 (no stars).
Frequency
Consequence
NM_003743.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NCOA1 | NM_003743.5 | c.222C>T | p.Val74Val | synonymous_variant | Exon 6 of 23 | ENST00000348332.8 | NP_003734.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000417 AC: 1AN: 239938Hom.: 0 AF XY: 0.00000768 AC XY: 1AN XY: 130180
GnomAD4 exome AF: 0.0000146 AC: 21AN: 1439852Hom.: 0 Cov.: 30 AF XY: 0.0000167 AC XY: 12AN XY: 716430
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151224Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73744
ClinVar
Submissions by phenotype
NCOA1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at