chr15-80450973-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PM2BP4
The NM_014862.4(ARNT2):āc.125G>Cā(p.Arg42Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000115 in 1,613,836 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R42C) has been classified as Uncertain significance.
Frequency
Consequence
NM_014862.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARNT2 | NM_014862.4 | c.125G>C | p.Arg42Pro | missense_variant | 2/19 | ENST00000303329.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARNT2 | ENST00000303329.9 | c.125G>C | p.Arg42Pro | missense_variant | 2/19 | 1 | NM_014862.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000717 AC: 18AN: 250992Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135704
GnomAD4 exome AF: 0.000120 AC: 176AN: 1461604Hom.: 0 Cov.: 31 AF XY: 0.000114 AC XY: 83AN XY: 727100
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2023 | The c.125G>C (p.R42P) alteration is located in exon 2 (coding exon 2) of the ARNT2 gene. This alteration results from a G to C substitution at nucleotide position 125, causing the arginine (R) at amino acid position 42 to be replaced by a proline (P). 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