NM_006540.4:c.3595G>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_006540.4(NCOA2):c.3595G>T(p.Ala1199Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000421 in 1,613,368 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 Uncertain significance (★).
Frequency
Consequence
NM_006540.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000282 AC: 7AN: 248506Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134838
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461134Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726888
GnomAD4 genome AF: 0.000197 AC: 30AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3595G>T (p.A1199S) alteration is located in exon 17 (coding exon 15) of the NCOA2 gene. This alteration results from a G to T substitution at nucleotide position 3595, causing the alanine (A) at amino acid position 1199 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