NM_024865.4:c.151+475C>A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024865.4(NANOG):c.151+475C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 151,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_024865.4 intron
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NANOG | ENST00000229307.9 | c.151+475C>A | intron_variant | Intron 1 of 3 | 1 | NM_024865.4 | ENSP00000229307.4 | |||
NANOG | ENST00000526286.1 | c.151+475C>A | intron_variant | Intron 1 of 3 | 1 | ENSP00000435288.1 | ||||
NANOG | ENST00000541267.5 | c.79+475C>A | intron_variant | Intron 3 of 5 | 5 | ENSP00000444434.1 | ||||
NANOG | ENST00000526434.2 | n.333+475C>A | intron_variant | Intron 1 of 1 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151928Hom.: 0 Cov.: 32 show subpopulations
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151928Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74208 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at