chr8-70121387-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_006540.4(NCOA2):c.4298A>G(p.Asn1433Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,610,496 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006540.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NCOA2 | NM_006540.4 | c.4298A>G | p.Asn1433Ser | missense_variant | 22/23 | ENST00000452400.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NCOA2 | ENST00000452400.7 | c.4298A>G | p.Asn1433Ser | missense_variant | 22/23 | 1 | NM_006540.4 | P1 | |
NCOA2 | ENST00000518363.2 | c.1676A>G | p.Asn559Ser | missense_variant | 10/11 | 2 | |||
NCOA2 | ENST00000518287.6 | c.*1330+2417A>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 244552Hom.: 0 AF XY: 0.0000151 AC XY: 2AN XY: 132394
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1458310Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3AN XY: 725130
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2024 | The c.4298A>G (p.N1433S) alteration is located in exon 22 (coding exon 20) of the NCOA2 gene. This alteration results from a A to G substitution at nucleotide position 4298, causing the asparagine (N) at amino acid position 1433 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at