chr8-124475225-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_007218.4(RNF139):c.116A>G(p.Asn39Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000211 in 1,613,338 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N39T) has been classified as Uncertain significance.
Frequency
Consequence
NM_007218.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF139 | NM_007218.4 | c.116A>G | p.Asn39Ser | missense_variant | 1/2 | ENST00000303545.4 | |
RNF139 | XM_047421310.1 | c.-414A>G | 5_prime_UTR_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF139 | ENST00000303545.4 | c.116A>G | p.Asn39Ser | missense_variant | 1/2 | 1 | NM_007218.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151836Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 250540Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135484
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461502Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727038
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 151836Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74124
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2024 | The c.116A>G (p.N39S) alteration is located in exon 1 (coding exon 1) of the RNF139 gene. This alteration results from a A to G substitution at nucleotide position 116, causing the asparagine (N) at amino acid position 39 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