chr8-70121387-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
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 -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NCOA2 | ENST00000452400.7 | c.4298A>G | p.Asn1433Ser | missense_variant | Exon 22 of 23 | 1 | NM_006540.4 | ENSP00000399968.2 | ||
NCOA2 | ENST00000518363.2 | c.1673A>G | p.Asn558Ser | missense_variant | Exon 10 of 11 | 2 | ENSP00000429132.2 | |||
NCOA2 | ENST00000518287.6 | n.*1330+2417A>G | intron_variant | Intron 20 of 20 | 5 | ENSP00000430148.2 |
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
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