rs2230783
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_181659.3(NCOA3):āc.2329T>Gā(p.Ser777Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000457 in 1,613,830 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_181659.3 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOA3 | NM_181659.3 | c.2329T>G | p.Ser777Ala | missense_variant | 12/23 | ENST00000371998.8 | |
NCOA3 | NM_001174087.2 | c.2329T>G | p.Ser777Ala | missense_variant | 12/23 | ||
NCOA3 | NM_006534.4 | c.2329T>G | p.Ser777Ala | missense_variant | 12/23 | ||
NCOA3 | NM_001174088.2 | c.2359T>G | p.Ser787Ala | missense_variant | 12/23 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA3 | ENST00000371998.8 | c.2329T>G | p.Ser777Ala | missense_variant | 12/23 | 1 | NM_181659.3 | P4 | |
NCOA3 | ENST00000372004.7 | c.2329T>G | p.Ser777Ala | missense_variant | 12/23 | 1 | A2 | ||
NCOA3 | ENST00000371997.3 | c.2359T>G | p.Ser787Ala | missense_variant | 12/23 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00246 AC: 375AN: 152132Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000691 AC: 172AN: 248834Hom.: 1 AF XY: 0.000542 AC XY: 73AN XY: 134676
GnomAD4 exome AF: 0.000248 AC: 362AN: 1461580Hom.: 2 Cov.: 32 AF XY: 0.000212 AC XY: 154AN XY: 727040
GnomAD4 genome ? AF: 0.00246 AC: 375AN: 152250Hom.: 2 Cov.: 32 AF XY: 0.00242 AC XY: 180AN XY: 74440
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at